6I7V

Ribosomal protein paralogs bL31 and bL36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 4YBB - determined by Noeske, J., Wasserman, M.R., Terry, D.S., Altman, R.B., Blanchard, S.C., Cate, J.H.D.  

Literature

Bacterial ribosome heterogeneity: Changes in ribosomal protein composition during transition into stationary growth phase.

Lilleorg, S.Reier, K.Pulk, A.Liiv, A.Tammsalu, T.Peil, L.Cate, J.D.Remme, J.

(2018) Biochimie 156: 169-180


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, BB
218Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsB
Find proteins for P0A7V0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, BC
206Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsC
Find proteins for P0A7V3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V3
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, BD
205Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsD (ramA)
Find proteins for P0A7V8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7V8
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, BE
150Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsE (spc)
Find proteins for P0A7W1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W1
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, BF
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsF
Find proteins for P02358 (Escherichia coli (strain K12))
Go to UniProtKB:  P02358
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, BG
151Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsG
Find proteins for P02359 (Escherichia coli (strain K12))
Go to UniProtKB:  P02359
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, BH
129Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0A7W7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7W7
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, BI
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsI
Find proteins for P0A7X3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7X3
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, BJ
98Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsJ (nusE)
Find proteins for P0A7R5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R5
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, BK
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsK
Find proteins for P0A7R9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R9
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, BM
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsM
Find proteins for P0A7S9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S9
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, BN
100Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsN
Find proteins for P0AG59 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG59
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, BO
88Escherichia coliMutation(s): 0 
Gene Names: rpsO
Find proteins for C3SSQ8 (Escherichia coli)
Go to UniProtKB:  C3SSQ8
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, BP
82Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsP
Find proteins for P0A7T3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, BQ
80Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsQ (neaA)
Find proteins for P0AG63 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG63
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, BR
55Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsR
Find proteins for P0A7T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7T7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, BS
79Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsS
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U3
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, BT
85Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsT
Find proteins for P0A7U7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7U7
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU, BU
54Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsU
Find proteins for P68679 (Escherichia coli (strain K12))
Go to UniProtKB:  P68679
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
BL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpsL (strA)
Find proteins for P0A7S3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7S3
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
CC, DC
271Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60422 (Escherichia coli (strain K12))
Go to UniProtKB:  P60422
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
CD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
CE, DE
201Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplD (eryA)
Find proteins for P60723 (Escherichia coli (strain K12))
Go to UniProtKB:  P60723
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
CF, DF
177Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplE
Find proteins for P62399 (Escherichia coli (strain K12))
Go to UniProtKB:  P62399
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
CG, DG
176Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0AG55 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG55
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
CH, DH
148Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplI
Find proteins for P0A7R1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7R1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
CJ, DJ
141Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplK (relC)
Find proteins for P0A7J7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7J7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
CK, DK
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplM
Find proteins for P0AA10 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AA10
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
CL, DL
123Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplN
Find proteins for P0ADY3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY3
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
CM, DM
144Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplO
Find proteins for P02413 (Escherichia coli (strain K12))
Go to UniProtKB:  P02413
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
CN, DN
136Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplP
Find proteins for P0ADY7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADY7
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
CO, DO
120Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplQ
Find proteins for P0AG44 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG44
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
CP, DP
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplR
Find proteins for P0C018 (Escherichia coli (strain K12))
Go to UniProtKB:  P0C018
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
CQ, DQ
114Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplS
Find proteins for P0A7K6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7K6
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
CR, DR
117Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplT (pdzA)
Find proteins for P0A7L3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L3
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
CS, DS
103Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplU
Find proteins for P0AG48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG48
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
CT, DT
110Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplV (eryB)
Find proteins for P61175 (Escherichia coli (strain K12))
Go to UniProtKB:  P61175
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
CU, DU
93Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplW
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ADZ0
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
CV, DV
102Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplX
Find proteins for P60624 (Escherichia coli (strain K12))
Go to UniProtKB:  P60624
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
CW, DW
94Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplY
Find proteins for P68919 (Escherichia coli (strain K12))
Go to UniProtKB:  P68919
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
CX, DX
76Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P0A7L8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7L8
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
CY, DY
77Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M2
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
CZ, DZ
62Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmC
Find proteins for P0A7M6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7M6
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
C0, D0
58Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmD
Find proteins for P0AG51 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AG51
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
C1, D1
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmF
Find proteins for P0A7N4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N4
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
C2, D2
51Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmG
Find proteins for P0A7N9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N9
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
C3, D3
46Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmH (rimA, ssaF)
Find proteins for P0A7P5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7P5
Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
C4, D4
64Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpmI
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Q1
Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36 2
C5, D5
45Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ykgO (rpmJ2)
Find proteins for Q2EEQ2 (Escherichia coli (strain K12))
Go to UniProtKB:  Q2EEQ2
Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
DD
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rplC
Find proteins for P60438 (Escherichia coli (strain K12))
Go to UniProtKB:  P60438
Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
D7
68Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ykgM (rpmE2)
Find proteins for P0A7N1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7N1
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosmal RNAAA1533Escherichia coli
Entity ID: 2
MoleculeChainsLengthOrganism
16S ribosomal RNABA1533Escherichia coli
Entity ID: 3
MoleculeChainsLengthOrganism
23S ribosomal RNADA2903Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
23S ribsomal RNACA2904Escherichia coli
Entity ID: 5
MoleculeChainsLengthOrganism
5S ribosomal RNADB,CB119Escherichia coli
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
D1, DA, DB, DR
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
BA, DA, DQ, DR, DS
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
AA, BA, C3, CA, CB, CM, CR, D5, DA, DB, DD, DM, DR
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

Download SDF File 
Download CCD File 
D5, DA, DM, DP
1,4-DIAMINOBUTANE
PUTRESCINE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
AA, D3, DA, DD, DS, DT, DU
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
GUN
Query on GUN

Download SDF File 
Download CCD File 
DA
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
D1, D3, DA, DP, DQ
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download SDF File 
Download CCD File 
DA
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
AA, DA, DE, DK, DN, DT
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
DA
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

Download SDF File 
Download CCD File 
DA
SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  18 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
AA, DA
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
AA, DA
RNA LINKINGC10 H16 N3 O8 PC
D2T
Query on D2T
AL
L-peptide linkingC5 H9 N O4 SASP
6MZ
Query on 6MZ
DA
RNA LINKINGC11 H16 N5 O7 PA
OMU
Query on OMU
DA
RNA LINKINGC10 H15 N2 O9 PU
1MG
Query on 1MG
DA
RNA LINKINGC11 H16 N5 O8 PG
OMC
Query on OMC
DA
RNA LINKINGC10 H16 N3 O8 PC
MA6
Query on MA6
AA
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
AA, DA
RNA LINKINGC11 H16 N5 O8 PG
G7M
Query on G7M
AA, DA
RNA LINKINGC11 H17 N5 O8 PG
UR3
Query on UR3
AA
RNA LINKINGC10 H15 N2 O9 PU
MEQ
Query on MEQ
DD
L-PEPTIDE LINKINGC6 H12 N2 O3GLN
OMG
Query on OMG
DA
RNA LINKINGC11 H16 N5 O8 PG
5MU
Query on 5MU
DA
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
DA
RNA LINKINGC11 H16 N5 O7 PA
4OC
Query on 4OC
AA
RNA LINKINGC11 H18 N3 O8 PC
3TD
Query on 3TD
DA
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
DA
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 212.020α = 90.00
b = 434.570β = 90.00
c = 623.130γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States--
Estonia--

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release