1NI3 | pdb_00001ni3

Structure of the Schizosaccharomyces pombe YchF GTPase

• PDB DOI: https://doi.org/10.2210/pdb1NI3/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-12-20 Released: 2003-01-07 
• Deposition Author(s): Kniewel, R.K., Buglino, J.A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.265 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structure of the S. pombe YchF GTP-binding protein

Kniewel, R.K., Buglino, J.A., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 44.87 kDa 
• Atom Count: 3,204 
• Modeled Residue Count: 378 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YchF GTP-binding protein	A	392	Schizosaccharomyces pombe	Mutation(s): 8  Gene Names: SPAC27E2.03C
UniProt
Find proteins for O13998 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O13998  Go to UniProtKB:  O13998

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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: 2.80 Å
• R-Value Free:  0.265 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.241	α = 90
b = 130.241	β = 90
c = 66.229	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-01-07 
Deposition Author(s): Kniewel, R.K., Buglino, J.A., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2003-01-07
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary