5ZT1

Structure of the bacterial pathogens ATPase with substrate ATP gamma S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.114 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insight Into Conformational Changes Induced by ATP Binding in a Type III Secretion-Associated ATPase FromShigella flexneri

Gao, X.Mu, Z.Yu, X.Qin, B.Wojdyla, J.Wang, M.Cui, S.

(2018) Front Microbiol 9: 1468-1468


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ATP synthase SpaL/MxiB
B, A
368Shigella flexneriMutation(s): 0 
Gene Names: spaL (mxiB, spa47)
EC: 7.1.2.2
Find proteins for P0A1C1 (Shigella flexneri)
Go to UniProtKB:  P0A1C1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AGS
Query on AGS

Download SDF File 
Download CCD File 
A
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
ATP-GAMMA-S; ADENOSINE 5'-(3-THIOTRIPHOSPHATE); ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE); ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.114 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.192 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 104.267α = 90.00
b = 104.267β = 90.00
c = 145.769γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PHENIXrefinement
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina81572005
National Natural Science Foundation of ChinaChina81401714

Revision History 

  • Version 1.0: 2018-05-16
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references
  • Version 1.2: 2018-08-22
    Type: Data collection, Database references