4YDE | pdb_00004yde

CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb4YDE/pdb

• Classification: TRANSFERASE
• Organism(s): Candida albicans SC5314
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-22 Released: 2016-07-06 
• Deposition Author(s): Kumar, S., Mabanglo, M.F., Hast, M.A., Shi, Y., Beese, L.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE

Kumar, S., Mabanglo, M.F., Hast, M.A., Shi, Y., Beese, L.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 106.51 kDa 
• Atom Count: 6,060 
• Modeled Residue Count: 714 
• Deposited Residue Count: 916 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha	A	329	Candida albicans SC5314	Mutation(s): 0  Gene Names: RAM2, CaO19.12280, CaO19.4817

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein farnesyltransferase/geranylgeranyltransferase type-1 Subunit beta	B	587	Candida albicans SC5314	Mutation(s): 0  Gene Names: RAM1, CaO19.12513

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4C7	E [auth B]	(3R,7S)-3,7,11-trimethyldodecyl trihydrogen diphosphate C15 H34 O7 P2 QLJFEPYMTKDKMH-LSDHHAIUSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.874	α = 90
b = 98.874	β = 90
c = 188.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Kumar, S., Mabanglo, M.F., Hast, M.A., Shi, Y., Beese, L.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2022-03-30
  Changes: Author supporting evidence, Database references
• Version 1.3: 2023-09-27
  Changes: Data collection, Refinement description