2P10

CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of hypothetical protein (NP_085906.1) from Mesorhizobium loti at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Mll9387 protein
A, B, C, D, E, F
A, B, C, D, E, F
286Mesorhizobium japonicum MAFF 303099Mutation(s): 11 
Gene Names: NP_085906.1mll9387
UniProt
Find proteins for Q981G2 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099))
Explore Q981G2 
Go to UniProtKB:  Q981G2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ981G2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
Q [auth B],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
BA [auth E],
CA [auth F],
G [auth A],
H [auth A],
I [auth A],
BA [auth E],
CA [auth F],
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth D],
J [auth A],
K [auth A],
P [auth B],
W [auth C],
AA [auth D],
J [auth A],
K [auth A],
P [auth B],
W [auth C],
X [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.165 
  • Space Group: H 3
  • Diffraction Data DOI: 10.18430/M32P10 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.269α = 90
b = 180.269β = 90
c = 185.514γ = 120
Software Package:
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description