3VEE

Rhodococcus jostii RHA1 DypB N246A variant in complex with heme

Structural Biology Knowledgebase: 3VEE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VEE

Classification: OXIDOREDUCTASE

Total Structure Weight: 114486.61

Macromolecule Entities
Molecule Chains Length Organism Details
DypB A, B, C 353 Rhodococcus jostii EC#: 1.11.1 IUBMB
Mutation: N246A
Gene Name(s): RHA1_ro02407
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B, C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FMT
Query on FMT

B FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.218
  • R-Value Work: 0.184
  • Space Group: P 32 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 132.75 α = 90.00
b = 132.75 β = 90.00
c = 160.60 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-01-07
  • Released Date: 2012-01-18
  • Deposition author(s): Grigg, J.C., Singh, R., Armstrong, Z., Eltis, L.D., Murphy, M.E.P.

Revision History

  • 2012-08-29
    Type: Citation | Details: Citation update