2ZZS

Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633

Akazaki, H.Kawai, F.Kumaki, Y.Sekine, K.Hakamata, W.Nishio, T.Park, S.-Y.Oku, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c554
AA [auth 1], BA [auth 2], CA [auth 3], DA [auth 4], EA [auth 5], FA [auth 6], A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
103Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VP2300
Find proteins for Q87MF5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87MF5 
Go to UniProtKB:  Q87MF5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download Ideal Coordinates CCD File 
AB [auth R] , CB [auth S] , DB [auth T] , EB [auth U] , FB [auth V] , GA [auth A] , GB [auth W] , HA [auth B] , 
AB [auth R],  CB [auth S],  DB [auth T],  EB [auth U],  FB [auth V],  GA [auth A],  GB [auth W],  HA [auth B],  HB [auth X],  IA [auth C],  IB [auth Y],  JB [auth Z],  KA [auth D],  KB [auth 1],  LA [auth E],  LB [auth 2],  MB [auth 3],  NA [auth F],  NB [auth 4],  OA [auth G],  OB [auth 5],  PA [auth H],  PB [auth 6],  QA [auth I],  RA [auth J],  SA [auth K],  TA [auth L],  UA [auth M],  VA [auth N],  WA [auth O],  XA [auth P],  ZA [auth Q]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BB [auth R], JA [auth C], MA [auth E], YA [auth P]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.949α = 71.5
b = 87.612β = 72.98
c = 103.847γ = 83.68
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance