7LVK

Cfr-modified 50S subunit from Escherichia coli


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Investigating antibiotic resistance of a ribosomal-RNA methylating enzyme through directed evolution

Tsai, K.Stojkovic, V.Noda-Garcia, L.Myasnikov, A.G.Young, I.D.Palla, A.Venkataramanan, S.Floor, S.Fraser, J.S.Frost, A.Tawfik, D.S.Fujimori, D.G.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth K]273Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60422 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth L]209Escherichia coliMutation(s): 0 
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth M]201Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth N]179Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth O]177Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9H [auth P]149Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13I [auth R]142Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AA10 (Escherichia coli (strain K12))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14J [auth S]123Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADY3 (Escherichia coli (strain K12))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15K [auth T]144Escherichia coliMutation(s): 0 
UniProt
Find proteins for P02413 (Escherichia coli (strain K12))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16L [auth U]136Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17M [auth V]127Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18N [auth W]117Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0C018 (Escherichia coli (strain K12))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19O [auth X]115Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7K6 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20P [auth Y]118Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21Q [auth Z]103Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG48 (Escherichia coli (strain K12))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22R [auth a]110Escherichia coliMutation(s): 0 
UniProt
Find proteins for P61175 (Escherichia coli (strain K12))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23S [auth b]100Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ADZ0 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24T [auth c]104Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25U [auth d]94Escherichia coliMutation(s): 0 
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27V [auth e]85Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7L8 (Escherichia coli (strain K12))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28W [auth f]78Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M2 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29X [auth g]63Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7M6 (Escherichia coli (strain K12))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30Y [auth h]59Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Z [auth i]57Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7N4 (Escherichia coli (strain K12))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AA [auth j]55Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34BA [auth k]46Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35CA [auth l]65Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36DA [auth m]38Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNAA [auth I]2,904Escherichia coli
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth J]120Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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CH [auth m]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth I]
AC [auth I]
AD [auth I]
AE [auth I]
AF [auth I]
AB [auth I],
AC [auth I],
AD [auth I],
AE [auth I],
AF [auth I],
AG [auth I],
AH [auth L],
BB [auth I],
BC [auth I],
BD [auth I],
BE [auth I],
BF [auth I],
BG [auth I],
BH [auth W],
CB [auth I],
CC [auth I],
CD [auth I],
CE [auth I],
CF [auth I],
CG [auth I],
DB [auth I],
DC [auth I],
DD [auth I],
DE [auth I],
DF [auth I],
DG [auth I],
EA [auth I],
EB [auth I],
EC [auth I],
ED [auth I],
EE [auth I],
EF [auth I],
EG [auth I],
FA [auth I],
FB [auth I],
FC [auth I],
FD [auth I],
FE [auth I],
FF [auth I],
FG [auth I],
GA [auth I],
GB [auth I],
GC [auth I],
GD [auth I],
GE [auth I],
GF [auth I],
GG [auth I],
HA [auth I],
HB [auth I],
HC [auth I],
HD [auth I],
HE [auth I],
HF [auth I],
HG [auth I],
IA [auth I],
IB [auth I],
IC [auth I],
ID [auth I],
IE [auth I],
IF [auth I],
IG [auth I],
JA [auth I],
JB [auth I],
JC [auth I],
JD [auth I],
JE [auth I],
JF [auth I],
JG [auth I],
KA [auth I],
KB [auth I],
KC [auth I],
KD [auth I],
KE [auth I],
KF [auth I],
KG [auth I],
LA [auth I],
LB [auth I],
LC [auth I],
LD [auth I],
LE [auth I],
LF [auth I],
LG [auth I],
MA [auth I],
MB [auth I],
MC [auth I],
MD [auth I],
ME [auth I],
MF [auth I],
MG [auth I],
NA [auth I],
NB [auth I],
NC [auth I],
ND [auth I],
NE [auth I],
NF [auth I],
NG [auth I],
OA [auth I],
OB [auth I],
OC [auth I],
OD [auth I],
OE [auth I],
OF [auth I],
OG [auth I],
PA [auth I],
PB [auth I],
PC [auth I],
PD [auth I],
PE [auth I],
PF [auth I],
PG [auth I],
QA [auth I],
QB [auth I],
QC [auth I],
QD [auth I],
QE [auth I],
QF [auth I],
QG [auth I],
RA [auth I],
RB [auth I],
RC [auth I],
RD [auth I],
RE [auth I],
RF [auth I],
RG [auth I],
SA [auth I],
SB [auth I],
SC [auth I],
SD [auth I],
SE [auth I],
SF [auth I],
SG [auth I],
TA [auth I],
TB [auth I],
TC [auth I],
TD [auth I],
TE [auth I],
TF [auth I],
TG [auth I],
UA [auth I],
UB [auth I],
UC [auth I],
UD [auth I],
UE [auth I],
UF [auth I],
UG [auth I],
VA [auth I],
VB [auth I],
VC [auth I],
VD [auth I],
VE [auth I],
VF [auth I],
VG [auth I],
WA [auth I],
WB [auth I],
WC [auth I],
WD [auth I],
WE [auth I],
WF [auth I],
WG [auth I],
XA [auth I],
XB [auth I],
XC [auth I],
XD [auth I],
XE [auth I],
XF [auth I],
XG [auth J],
YA [auth I],
YB [auth I],
YC [auth I],
YD [auth I],
YE [auth I],
YF [auth I],
YG [auth K],
ZA [auth I],
ZB [auth I],
ZC [auth I],
ZD [auth I],
ZE [auth I],
ZF [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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ZG [auth K]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
4D4
Query on 4D4
L [auth U]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcisTEM1.0.0

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI137270

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations