3IWT | pdb_00003iwt

Structure of hypothetical molybdenum cofactor biosynthesis protein B from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb3IWT/pdb
• Entry: 3IWT supersedes: 2PJK

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-03 Released: 2009-09-29 
• Deposition Author(s): Antonyuk, S.V., Ellis, M.J., Strange, R.W., Hasnain, S.S., Bessho, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Structure of hypothetical Mo-cofactor biosynthesis protein B (ST2315) from Sulfolobus tokodaii

Antonyuk, S.V., Strange, R.W., Ellis, M.J., Bessho, Y., Kuramitsu, S., Shinkai, A., Yokoyama, S., Hasnain, S.S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1200-1203

• PubMed: 20054111 
• DOI: https://doi.org/10.1107/S1744309109043772
• Primary Citation of Related Structures:  
  3IWT


• PubMed Abstract: 
  

  The structure of a probable Mo-cofactor biosynthesis protein B from Sulfolobus tokodaii, belonging to space group P6(4)22 with unit-cell parameters a = b = 136.68, c = 210.52 A, was solved by molecular replacement to a resolution of 1.9 A and refined to an R factor and R(free) of 16.8% and 18.5%, respectively. The asymmetric unit contains a trimer, while the biologically significant oligomer is predicted to be a hexamer by size-exclusion chromatography. The subunit structure and fold of ST2315 are similar to those of other enzymes that are known to be involved in the molybdopterin- and molybdenum cofactor-biosynthesis pathways.

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Organizational Affiliation: 

Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England.

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 (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.29 kDa 
• Atom Count: 4,698 
• Modelled Residue Count: 498 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
178aa long hypothetical molybdenum cofactor biosynthesis protein B	A, B, C	178	Sulfurisphaera tokodaii	Mutation(s): 0  Gene Names: ST2315
UniProt
Find proteins for Q96Y52 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96Y52  Go to UniProtKB:  Q96Y52

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], H [auth B], I [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	F [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.675	α = 90
b = 136.675	β = 90
c = 210.525	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Antonyuk, S.V., Ellis, M.J., Strange, R.W., Hasnain, S.S., Bessho, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2PJK

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description