4LF7

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus

Demirci, H.Belardinelli, R.Carr, J.Murphy IV, F.Jogl, G.Dahlberg, A.E.Gregory, S.T.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S2B256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsBrps2TTHA0861
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S3C239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsCrps3TTHA1686
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S4D209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsDrps4TTHA1665
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S5E162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsETTHA1675
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S6F101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsFTTHA0245
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S7G156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsGrps7TTHA1696
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S8H138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsHTTHA1678
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S9I128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsIrps9TTHA1464
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S10J105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJTTHA1693
UniProt
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S11K129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsKrps11TTHA1666
UniProt
Find proteins for P80376 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S12L135Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S13M126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsMrps13TTHA1667
UniProt
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S14N61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZrpsNTTHA1679
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S15O89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsOTTHA1138
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S16P88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsPTTHA1035
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S17Q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQTTHA1683
UniProt
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S18R88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsRTTHA0243
UniProt
Find proteins for Q5SLQ0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S19S93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsSTTHA1688
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein S20T106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsTrps20TTHA1397
UniProt
Find proteins for P80380 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
ribosomal protein THXU27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsUTTHA1396
UniProt
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA1,522Thermus thermophilus HB8
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAR
Query on PAR

Download Ideal Coordinates CCD File 
AI [auth A],
BI [auth A],
CI [auth A],
DI [auth A],
EI [auth A],
AI [auth A],
BI [auth A],
CI [auth A],
DI [auth A],
EI [auth A],
WH [auth A],
XH [auth A],
YH [auth A],
ZH [auth A]
PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
HI [auth D],
RI [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
DF [auth A],
EF [auth A],
FF [auth A],
GF [auth A],
HF [auth A],
DF [auth A],
EF [auth A],
FF [auth A],
GF [auth A],
HF [auth A],
IF [auth A],
JF [auth A],
KF [auth A],
LF [auth A],
MF [auth A],
MI [auth E],
NF [auth A],
OF [auth A],
PF [auth A],
QF [auth A],
RF [auth A],
SF [auth A],
TF [auth A],
UF [auth A],
VF [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DG [auth A],
DH [auth A],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EG [auth A],
EH [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FG [auth A],
FH [auth A],
FI [auth B],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GG [auth A],
GH [auth A],
GI [auth C],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HG [auth A],
HH [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IG [auth A],
IH [auth A],
II [auth D],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JG [auth A],
JH [auth A],
JI [auth D],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KG [auth A],
KH [auth A],
KI [auth D],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LG [auth A],
LH [auth A],
LI [auth E],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MG [auth A],
MH [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NG [auth A],
NH [auth A],
NI [auth G],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OG [auth A],
OH [auth A],
OI [auth H],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PG [auth A],
PH [auth A],
PI [auth L],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QG [auth A],
QH [auth A],
QI [auth M],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RG [auth A],
RH [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SG [auth A],
SH [auth A],
SI [auth N],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TG [auth A],
TH [auth A],
TI [auth T],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UG [auth A],
UH [auth A],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VG [auth A],
VH [auth A],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
0TD
Query on 0TD
L L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 402.445α = 90
b = 402.445β = 90
c = 176.924γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-02
    Type: Initial release