3M1A | pdb_00003m1a

The Crystal Structure of a Short-chain Dehydrogenase from Streptomyces avermitilis to 2A

PDB DOI: https://doi.org/10.2210/pdb3M1A/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces avermitilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-03-04 Released: 2010-03-23
Deposition Author(s): Stein, A.J., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.197 (Depositor), 0.198 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3M1A

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

Literature

The Crystal Structure of a Short-chain Dehydrogenase from Streptomyces avermitilis to 2A

Stein, A.J., Evdokimova, E., Egorova, O., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 298.55 kDa
Atom Count: 20,905
Modeled Residue Count: 2,703
Deposited Residue Count: 2,810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	281	Streptomyces avermitilis	Mutation(s): 1 Gene Names: SAV770, SAV_770
UniProt
Find proteins for Q82PV2 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82PV2 Go to UniProtKB: Q82PV2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q82PV2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain P [auth I] SDF format, chain O [auth E] MOL2 format, chain P [auth I] MOL2 format, chain O [auth E] mmCIF format, chain P [auth I] mmCIF format, chain O [auth E]	O [auth E], P [auth I]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain O [auth E] Focus chain P [auth I] Interactions & Density Focus chain O [auth E] Focus chain P [auth I]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A], L [auth B], M [auth D], N [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth E] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth D] Focus chain N [auth E]

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, I, J	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.242 (Depositor), 0.242 (DCC)
R-Value Work: 0.197 (Depositor), 0.198 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.638	α = 90
b = 202.779	β = 90
c = 106.339	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
DM	phasing
BUCCANEER	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2024-11-20
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.