3MTJ | pdb_00003mtj

The Crystal Structure of a Homoserine Dehydrogenase from Thiobacillus denitrificans to 2.15A

PDB DOI: https://doi.org/10.2210/pdb3MTJ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thiobacillus denitrificans ATCC 25259
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-04-30 Released: 2010-05-12
Deposition Author(s): Stein, A.J., Cui, H., Chin, S., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.256 (Depositor), 0.252 (DCC)
R-Value Work:
0.217 (Depositor), 0.216 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The Crystal Structure of a Homoserine Dehydrogenase from Thiobacillus denitrificans to 2.15A

Stein, A.J., Cui, H., Chin, S., Savchenko, A., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 48.68 kDa
Atom Count: 3,338
Modeled Residue Count: 431
Deposited Residue Count: 444
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A	444	Thiobacillus denitrificans ATCC 25259	Mutation(s): 0 Gene Names: Tbd_0843 EC: 1.1.1.3
UniProt
Find proteins for Q3SKI5 (Thiobacillus denitrificans (strain ATCC 25259 / T1)) Explore Q3SKI5 Go to UniProtKB: Q3SKI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3SKI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.256 (Depositor), 0.252 (DCC)
R-Value Work: 0.217 (Depositor), 0.216 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.613	α = 90
b = 67.613	β = 90
c = 224.279	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-05-12

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-05-12
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: 2024-11-06
Changes: Data collection, Database references, Derived calculations, 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.