2EJW | pdb_00002ejw

Homoserine Dehydrogenase from Thermus thermophilus HB8

PDB DOI: https://doi.org/10.2210/pdb2EJW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-21 Released: 2008-02-12
Deposition Author(s): Omi, R., Goto, M., Miyahara, I., Hirotsu, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.238 (Depositor), 0.239 (DCC)
R-Value Work:
0.210 (Depositor), 0.212 (DCC)
R-Value Observed:
0.210 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Homoserine Dehydrogenase from Thermus thermophilus HB8

Omi, R., Goto, M., Miyahara, I., Hirotsu, K.

To be published.

Macromolecule Content

Total Structure Weight: 142.66 kDa
Atom Count: 10,940
Modeled Residue Count: 1,324
Deposited Residue Count: 1,328
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A, B, C [auth E], D [auth F]	332	Thermus thermophilus HB8	Mutation(s): 0 EC: 1.1.1.3
UniProt
Find proteins for Q5SL04 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL04 Go to UniProtKB: Q5SL04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SL04
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain J [auth B] MOL2 format, chain N [auth E] MOL2 format, chain J [auth B] mmCIF format, chain N [auth E] mmCIF format, chain J [auth B]	J [auth B], N [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth E] Interactions & Density Focus chain J [auth B] Focus chain N [auth E]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain M [auth E] SDF format, chain G [auth A] MOL2 format, chain P [auth F] MOL2 format, chain M [auth E] MOL2 format, chain G [auth A] mmCIF format, chain P [auth F] mmCIF format, chain M [auth E] mmCIF format, chain G [auth A]	G [auth A], M [auth E], P [auth F]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth E] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain M [auth E] Focus chain P [auth F]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain L [auth E] SDF format, chain K [auth E] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth F] MOL2 format, chain L [auth E] MOL2 format, chain K [auth E] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth F] mmCIF format, chain L [auth E] mmCIF format, chain K [auth E] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth E] E [auth A], F [auth A], H [auth B], I [auth B], K [auth E], L [auth E], O [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth F] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth E] Focus chain L [auth E] Focus chain O [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.238 (Depositor), 0.239 (DCC)
R-Value Work: 0.210 (Depositor), 0.212 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 165.439	α = 90
b = 173.603	β = 90
c = 97.123	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-02-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations