6O62 | pdb_00006o62

Crystal structure of Sec4p, a Rab family GTPase from Candida albicans

• PDB DOI: https://doi.org/10.2210/pdb6O62/pdb

• Classification: PROTEIN BINDING
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-05 Released: 2019-04-03 
• Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.315 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

To be published

Stogios, P.J.

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: 21.27 kDa 
• Atom Count: 1,559 
• Modeled Residue Count: 169 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein SEC4	A	184	Candida albicans SC5314	Mutation(s): 0  Gene Names: SEC4, CAALFM_CR01750CA, Ca49C4.03c, CaO19.10103, CaO19.2571
UniProt
Find proteins for P0CY31 (Candida albicans (strain SC5314 / ATCC MYA-2876)) Explore P0CY31  Go to UniProtKB:  P0CY31

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.315 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.301	α = 90
b = 38.082	β = 105.09
c = 43.115	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Stogios, P.J., Skarina, T., Di Leo, R., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description