4LFC

Crystal Structure of 30S ribosomal subunit from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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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UniProt GroupP80371
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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
Find proteins for P0DOY9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupP0DOY9
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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
Find proteins for Q5SHN7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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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
Find proteins for P0DOY6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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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
UniProt
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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
Find proteins for Q5SIH3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SIH3
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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
TOY
Query on TOY

Download Ideal Coordinates CCD File 
CF [auth A]TOBRAMYCIN
C18 H37 N5 O9
NLVFBUXFDBBNBW-PBSUHMDJSA-N
 Ligand Interaction
ZN
Query on ZN

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EF [auth D],
MF [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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AE [auth A],
BE [auth A],
CE [auth A],
DE [auth A],
EE [auth A],
AE [auth A],
BE [auth A],
CE [auth A],
DE [auth A],
EE [auth A],
FE [auth A],
QD [auth A],
RD [auth A],
SD [auth A],
TD [auth A],
UD [auth A],
VD [auth A],
WD [auth A],
XD [auth A],
YD [auth A],
ZD [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],
AF [auth A],
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AF [auth A],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BF [auth A],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
DA [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DF [auth B],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FF [auth D],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth D],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth E],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth H],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth J],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth K],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth M],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth N],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth N],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth Q],
QA [auth A],
QB [auth A],
QC [auth A],
QE [auth A],
QF [auth S],
RA [auth A],
RB [auth A],
RC [auth A],
RE [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SE [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TE [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UE [auth A],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VE [auth A],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WE [auth A],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XE [auth A],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YE [auth A],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZE [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: 3.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 401.831α = 90
b = 401.831β = 90
c = 175.888γ = 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