3JZD | pdb_00003jzd

Crystal structure of Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution

PDB DOI: https://doi.org/10.2210/pdb3JZD/pdb

Classification: OXIDOREDUCTASE
Organism(s): Cupriavidus pinatubonensis JMP134
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-09-23 Released: 2009-10-06
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.210 (Depositor), 0.211 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.176 (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 Putative alcohol dehedrogenase (YP_298327.1) from RALSTONIA EUTROPHA JMP134 at 2.10 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 155.05 kDa
Atom Count: 11,566
Modeled Residue Count: 1,416
Deposited Residue Count: 1,432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-containing alcohol dehydrogenase	A, B, C, D	358	Cupriavidus pinatubonensis JMP134	Mutation(s): 0 Gene Names: Reut_B4129, YP_298327.1 EC: 1.3.1.32
UniProt
Find proteins for Q46TQ1 (Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197)) Explore Q46TQ1 Go to UniProtKB: Q46TQ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q46TQ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B]	E [auth A], L [auth B], P [auth C], U [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain U [auth D]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain X [auth D] MOL2 format, chain R [auth C] MOL2 format, chain X [auth D] mmCIF format, chain R [auth C] mmCIF format, chain X [auth D]	R [auth C], X [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain R [auth C] Focus chain X [auth D]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A]	K [auth A], O [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Interactions & Density Focus chain K [auth A] Focus chain O [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain W [auth D] MOL2 format, chain W [auth D] mmCIF format, chain W [auth D]	W [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain W [auth D] Interactions & Density Focus chain W [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], J [auth A], N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain S [auth C]	S [auth C], T [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B]	H [auth A], M [auth B], Q [auth C], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain V [auth D]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.210 (Depositor), 0.211 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.841	α = 90
b = 143.841	β = 90
c = 169.011	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-11-06
Changes: Data collection, Refinement description, Structure summary