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- PDB-4yde: CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE... -

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Basic information

Entry
Database: PDB / ID: 4yde
TitleCRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE
Components(Protein farnesyltransferase/geranylgeranyltransferase type-1 ...) x 2
KeywordsTRANSFERASE / Farnesyl transferase
Function / homology
Function and homology information


Protein prenylyltransferase / Glycosyltransferase - #20 / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKumar, S. / Mabanglo, M.F. / Hast, M.A. / Shi, Y. / Beese, L.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF CANDIDA ALBICANS PROTEIN FARNESYLTRANSFERASE BINARY COMPLEX WITH THE ISOPRENOID FARNESYLDIPHOSPHATE
Authors: Kumar, S. / Mabanglo, M.F. / Hast, M.A. / Shi, Y. / Beese, L.S.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
B: Protein farnesyltransferase/geranylgeranyltransferase type-1 Subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5086
Polymers105,9302
Non-polymers5784
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-64 kcal/mol
Surface area29530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.874, 98.874, 188.616
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

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Protein farnesyltransferase/geranylgeranyltransferase type-1 ... , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha


Mass: 39236.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: RAM2, CaO19.12280, CaO19.4817 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5APE8
#2: Protein Protein farnesyltransferase/geranylgeranyltransferase type-1 Subunit beta


Mass: 66693.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: RAM1, CaO19.12513 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59LE1

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Non-polymers , 4 types, 154 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-4C7 / (3R,7S)-3,7,11-trimethyldodecyl trihydrogen diphosphate


Mass: 388.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H34O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 9%-13% PEG 2050 chips, 100 mM HEPES pH 7.2 100 -200 mM CaCl2, 5 uM ZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→47.82 Å / Num. obs: 26416 / % possible obs: 100 % / Redundancy: 14.5 % / Rsym value: 0.118 / Net I/σ(I): 31.1
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L9P

4l9p


Resolution: 2.701→47.822 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 2000 7.57 %Random selection
Rwork0.1946 ---
obs0.1972 26410 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→47.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 33 150 6060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036054
X-RAY DIFFRACTIONf_angle_d0.5748199
X-RAY DIFFRACTIONf_dihedral_angle_d12.3362211
X-RAY DIFFRACTIONf_chiral_restr0.023890
X-RAY DIFFRACTIONf_plane_restr0.0031038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7015-2.7690.29331380.25481683X-RAY DIFFRACTION99
2.769-2.84390.30941390.25161703X-RAY DIFFRACTION100
2.8439-2.92760.26431410.2341710X-RAY DIFFRACTION100
2.9276-3.0220.29361390.24921705X-RAY DIFFRACTION100
3.022-3.130.30671410.23741720X-RAY DIFFRACTION100
3.13-3.25530.27361410.23281720X-RAY DIFFRACTION100
3.2553-3.40350.24131420.22211734X-RAY DIFFRACTION100
3.4035-3.58280.22911400.20931714X-RAY DIFFRACTION100
3.5828-3.80720.2321430.18611743X-RAY DIFFRACTION100
3.8072-4.1010.2141430.1671747X-RAY DIFFRACTION100
4.101-4.51350.20211440.15261753X-RAY DIFFRACTION100
4.5135-5.16590.17151440.15291764X-RAY DIFFRACTION100
5.1659-6.50590.23051480.19361799X-RAY DIFFRACTION100
6.5059-47.82910.1961570.18721915X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.83960.0611-0.00551.70420.79232.20990.2002-0.06350.0706-0.04-0.07720.0677-0.02150.0257-0.12150.2266-0.02190.0550.2996-0.05910.272930.583190.73976.4387
21.62980.2589-0.29891.78490.20031.87940.1762-0.1764-0.20040.3875-0.06090.17830.5047-0.1195-0.08860.4198-0.1184-0.00410.32710.03710.268624.099876.706320.5631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 2 through 304)
2X-RAY DIFFRACTION2(chain 'B' and resid 110 through 580)

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