3IV6 | pdb_00003iv6

Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.

PDB DOI: https://doi.org/10.2210/pdb3IV6/pdb

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

Deposited: 2009-08-31 Released: 2009-09-15
Deposition Author(s): Kim, Y., Marshall, N., Keigher, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.238 (Depositor), 0.233 (DCC)
R-Value Work:
0.176 (Depositor), 0.173 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of Putative Zn-dependent Alcohol Dehydrogenases from Rhodobacter sphaeroides.

Kim, Y., Marshall, N., Keigher, L., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 119.53 kDa
Atom Count: 8,466
Modeled Residue Count: 1,016
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Zn-dependent Alcohol Dehydrogenase	A, B, C, D	261	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: RHOS4_40580, RSP_4162
UniProt
Find proteins for Q3IV08 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3IV08 Go to UniProtKB: Q3IV08
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3IV08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain I [auth C] SDF format, chain J [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain I [auth C] MOL2 format, chain J [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain I [auth C] mmCIF format, chain J [auth D]	E [auth A], F [auth B], I [auth C], J [auth D]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	G [auth B], H [auth B], K [auth D], L [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth B] Focus chain K [auth D] Focus chain L [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: 2.70 Å
R-Value Free: 0.238 (Depositor), 0.233 (DCC)
R-Value Work: 0.176 (Depositor), 0.173 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.883	α = 90
b = 179.883	β = 90
c = 83.826	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-09-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary