3DO5 | pdb_00003do5

Crystal structure of Putative Homoserine Dehydrogenase (NP_069768.1) from ARCHAEOGLOBUS FULGIDUS at 2.20 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DO5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-03 Released: 2008-09-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal structure of Putative Homoserine Dehydrogenase (NP_069768.1) from ARCHAEOGLOBUS FULGIDUS at 2.20 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.25 kDa 
• Atom Count: 2,511 
• Modeled Residue Count: 320 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Homoserine dehydrogenase	A	327	Archaeoglobus fulgidus	Mutation(s): 0  Gene Names: NP_069768.1, AF_0935 EC: 1.1.1.3
UniProt
Find proteins for O29327 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29327  Go to UniProtKB:  O29327

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4	B [auth A], C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33DO5

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.107	α = 90
b = 120.818	β = 90
c = 57.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-09-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary