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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.252 (Depositor), 0.248 (DCC)
R-Value Work:
0.195 (Depositor), 0.198 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

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

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3IWN8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.252 (Depositor), 0.248 (DCC)
R-Value Work: 0.195 (Depositor), 0.198 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data:

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-07-01

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

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

Revision History (Full details and data files)

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