3PM9 | pdb_00003pm9

Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution

PDB DOI: https://doi.org/10.2210/pdb3PM9/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-16 Released: 2010-12-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.227 (Depositor), 0.220 (DCC)
R-Value Work:
0.193 (Depositor), 0.190 (DCC)
R-Value Observed:
0.195 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 313.79 kDa
Atom Count: 22,350
Modeled Residue Count: 2,790
Deposited Residue Count: 2,856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D, E A, B, C, D, E, F	476	Rhodopseudomonas palustris	Mutation(s): 0 Gene Names: RPA1076
UniProt
Find proteins for Q6NAV4 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6NAV4 Go to UniProtKB: Q6NAV4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NAV4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth F] SDF format, chain AA [auth E] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] FA [auth F] G [auth A] L [auth B] Q [auth C] AA [auth E], FA [auth F], G [auth A], L [auth B], Q [auth C], V [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain AA [auth E] Focus chain FA [auth F] Focus chain G [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain I [auth A] SDF format, chain HA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E]	CA [auth E] DA [auth E] EA [auth E] HA [auth F] I [auth A] CA [auth E], DA [auth E], EA [auth E], HA [auth F], I [auth A], IA [auth F], J [auth A], JA [auth F], K [auth A], N [auth B], O [auth B], P [auth B], S [auth C], T [auth C], U [auth C], X [auth D], Y [auth D], Z [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth D] Focus chain Z [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	BA [auth E] GA [auth F] H [auth A] M [auth B] R [auth C] BA [auth E], GA [auth F], H [auth A], M [auth B], R [auth C], W [auth D]	Unknown ligand NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain BA [auth E] Focus chain GA [auth F] Focus chain H [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain W [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.227 (Depositor), 0.220 (DCC)
R-Value Work: 0.193 (Depositor), 0.190 (DCC)
R-Value Observed: 0.195 (Depositor)

Diffraction Data:

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.085	α = 90
b = 250.728	β = 90
c = 251.711	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-07-20
Changes: Structure summary
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-27
Changes: Data collection, Refinement description, Structure summary