1VP8 | pdb_00001vp8

CRYSTAL STRUCTURE OF an alpha/beta domain of a putative pyruvate kinase (AF0103) FROM ARCHAEOGLOBUS FULGIDUS DSM 4304 AT 1.30 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1VP8/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-14 Released: 2004-10-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.166 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Crystal structure of hypothetical protein (NP_068944.1) from Archaeoglobus fulgidus at 1.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 23.15 kDa 
• Atom Count: 1,703 
• Modeled Residue Count: 190 
• Deposited Residue Count: 201 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein AF0103	A	201	Archaeoglobus fulgidus DSM 4304	Mutation(s): 7  Gene Names: NP_068944.1
UniProt
Find proteins for O30133 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30133  Go to UniProtKB:  O30133

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
UNL	C [auth A]	Unknown ligand FVTCRASFADXXNN-SCRDCRAPSA-N

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: 1.30 Å
• R-Value Free:  0.166 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VP8

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.65	α = 90
b = 109.65	β = 90
c = 76.451	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-10-26
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-16
  Changes: Data collection, Structure summary