4ZQB | pdb_00004zqb

Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate

• PDB DOI: https://doi.org/10.2210/pdb4ZQB/pdb

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


• Deposited: 2015-05-08 Released: 2015-05-20 
• Deposition Author(s): Kowiel, M., Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Porebski, P.J., Bonanno, J., Almo, S.C., Minor, W., New York Structural Genomics Research Consortium (NYSGRC)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate

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: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

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: 70.78 kDa 
• Atom Count: 5,653 
• Modeled Residue Count: 629 
• 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], F [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
PGE	E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	K [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], G [auth B], H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.200 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.489	α = 90
b = 71.489	β = 90
c = 244.364	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-20 
Deposition Author(s): Kowiel, M., Gasiorowska, O.A., Shabalin, I.G., Handing, K.B., Porebski, P.J., 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/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2015-05-20
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2022-04-13
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Refinement description