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
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S2256Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80371 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S3239Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S4209Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S5162Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S6101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SLP8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S7156Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P17291 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S8138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S9128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S10105Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S11129Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S12135Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for F6DEQ7 (Thermus thermophilus (strain SG0.5JP17-16))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S13126Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1461Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1589Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SJ76 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1688Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S17105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1888Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S1993Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein S20106Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ribosomal protein THX27Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNA1,522Thermus thermophilus HB8
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Small Molecules
Ligands 4 Unique
IDChains Name / 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
ZN
Query on ZN

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HI [auth D],
RI [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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
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
Modified Residues  1 Unique
IDChains TypeFormula2D 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