4H3V | pdb_00004h3v

Crystal structure of oxidoreductase domain protein from Kribbella flavida

• PDB DOI: https://doi.org/10.2210/pdb4H3V/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Kribbella flavida DSM 17836
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-14 Released: 2012-09-26 
• Deposition Author(s): Michalska, K., Mack, J.C., McKnight, S.M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.177 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal structure of oxidoreductase domain protein from Kribbella flavida

Michalska, K., Mack, J.C., McKnight, S.M., Endres, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 84.45 kDa 
• Atom Count: 6,366 
• Modeled Residue Count: 760 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase domain protein	A, B	390	Kribbella flavida DSM 17836	Mutation(s): 0  Gene Names: Kfla_4276
UniProt
Find proteins for D2PU28 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Explore D2PU28  Go to UniProtKB:  D2PU28

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth A], E [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free:  0.177 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34H3V

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.597	α = 90
b = 70.597	β = 90
c = 288.538	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELX	model building
MLPHARE	phasing
DM	model building
BUCCANEER	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Michalska, K., Mack, J.C., McKnight, S.M., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary