5C5I | pdb_00005c5i

Crystal structure of NADP-dependent dehydrogenase from Rhodobacter sphaeroides

• PDB DOI: https://doi.org/10.2210/pdb5C5I/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cereibacter sphaeroides 2.4.1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-06-19 Released: 2015-07-01 
• Deposition Author(s): Kowiel, M., Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Porebski, P.J., Cymborowski, M., Al Obaidi, N.F., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of NADP-dependent dehydrogenase from Rhodobacter sphaeroides

Kowiel, M., Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Porebski, P.J., Bonanno, J., Almo, S.C., Minor, W.

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: 68.56 kDa 
• Atom Count: 4,664 
• Modeled Residue Count: 620 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP-dependent dehydrogenase	A, B	316	Cereibacter sphaeroides 2.4.1	Mutation(s): 0  Gene Names: RSP_3442 EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
UniProt
Find proteins for Q3IWN8 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IWN8  Go to UniProtKB:  Q3IWN8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.252 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3KS38

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.048	α = 90
b = 80.085	β = 93.69
c = 61.33	γ = 90

Software Package:

Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	phasing
HKL-3000	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Kowiel, M., Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Porebski, P.J., Cymborowski, M., Al Obaidi, N.F., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)

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Funding Organization	Location	Grant Number
National Institutes of Health	United States	--

Revision History  

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Refinement description