4DAL | pdb_00004dal

Crystal structure of Putative aldehyde dehydrogenase from Sinorhizobium meliloti 1021

PDB DOI: https://doi.org/10.2210/pdb4DAL/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti 1021
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-01-12 Released: 2012-03-14
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.237 (Depositor), 0.244 (DCC)
R-Value Work:
0.184 (Depositor), 0.200 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Putative aldehyde dehydrogenase from Sinorhizobium meliloti 1021

Malashkevich, V.N., Bhosle, R., Toro, R., Seidel, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 436.44 kDa
Atom Count: 29,632
Modeled Residue Count: 3,806
Deposited Residue Count: 3,984
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aldehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	498	Sinorhizobium meliloti 1021	Mutation(s): 0 Gene Names: R02268, SMc01656 EC: 1.2.1
UniProt
Find proteins for Q92ND9 (Rhizobium meliloti (strain 1021)) Explore Q92ND9 Go to UniProtKB: Q92ND9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92ND9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth D]	I [auth A], J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [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, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.237 (Depositor), 0.244 (DCC)
R-Value Work: 0.184 (Depositor), 0.200 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.463	α = 90
b = 150.745	β = 102.13
c = 159.569	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-14

Deposition Author(s):

Malashkevich, V.N.

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2012-03-14
Type: Initial release
Version 1.1: 2014-04-02
Changes: Other
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2023-12-06
Changes: Data collection
Version 1.4: 2024-11-27
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.