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 5XYM | pdb_00005xym

Large subunit of Mycobacterium smegmatis

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 5XYM

This is version 1.2 of the entry. See complete history. 

Literature

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers.

Li, Z., Ge, X., Zhang, Y., Zheng, L., Sanyal, S., Gao, N.

(2018) Protein Cell 9: 384-388

  • DOI: https://doi.org/10.1007/s13238-017-0456-9
  • Primary Citation Related Structures: 
    5XYM, 5XYU
    • Organizational Affiliation: 
    • State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, 100871, China.

Macromolecule Content 

  • Total Structure Weight: 1,462.03 kDa 
  • Atom Count: 84,069 
  • Modeled Residue Count: 5,903 
  • Deposited Residue Count: 6,880 
  • Unique protein chains: 29
  • Unique nucleic acid chains: 2

Macromolecules


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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32A [auth 0]57Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33 2B [auth 1]54Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0R551 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34C [auth 2]47Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35D [auth 3]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36E [auth 4]37Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2H [auth C]278Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3I [auth D]217Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4J [auth E]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5K [auth F]187Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6L [auth G]179Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L9M [auth H]151Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13N [auth J]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14O [auth K]122Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15P [auth L]147Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16Q [auth M]138Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17R [auth N]199Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18S [auth O]127Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19T [auth P]113Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
Find proteins for A0QV42 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20U [auth Q]129Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21V [auth R]103Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22W [auth S]153Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23X [auth T]100Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24Y [auth U]105Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L25Z [auth V]215Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27AA [auth W]88Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L28BA [auth X]64Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29CA [auth Y]77Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30DA [auth Z]61Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein bL37EA [auth a]24Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains LengthOrganismImage
23S RNAF [auth A]3,164Mycolicibacterium smegmatis MC2 155
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Entity ID: 7
MoleculeChains LengthOrganismImage
5S RNAG [auth B]118Mycolicibacterium smegmatis MC2 155
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MG

Query on MG


Download:Ideal Coordinates CCD File
AB [auth A]
AC [auth A]
AD [auth A]
AE [auth A]
AF [auth A]
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references, Derived calculations, Structure summary