3L6D

Crystal structure of putative oxidoreductase from Pseudomonas putida KT2440

• PDB DOI: https://doi.org/10.2210/pdb3L6D/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-23 Released: 2010-01-12 
• Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.260 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 

Literature

Crystal structure of putative oxidoreductase from Pseudomonas putida KT2440

Malashkevich, V.N., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.75 kDa 
• Atom Count: 4,780 
• Modelled Residue Count: 588 
• Deposited Residue Count: 612 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B	306	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: NP_744942.1, PP2798
UniProt
Find proteins for Q88J51 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88J51  Go to UniProtKB:  Q88J51

Small Molecules

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: 1.90 Å
• R-Value Free: 0.260 
• R-Value Work: 0.208 
• R-Value Observed: 0.211 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.342	α = 90
b = 37.647	β = 93.35
c = 104.252	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Malashkevich, V.N., Patskovsky, Y., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-10-24
  Changes: Database references, Structure summary
• Version 1.3: 2015-05-20
  Changes: Database references
• Version 1.4: 2017-11-01
  Changes: Refinement description
• Version 1.5: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary