2ZZS | pdb_00002zzs

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 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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This is version 1.3 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c554103Vibrio parahaemolyticus RIMD 2210633Mutation(s): 0 
Gene Names: VP2300
UniProt
Find proteins for Q87MF5 (Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
Explore Q87MF5 
Go to UniProtKB:  Q87MF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ87MF5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / 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]
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
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary