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- PDB-5hna: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 5hna
TitleCrystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1251
ComponentsFarnesyl pyrophosphate synthase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / membrane / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-63D / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.693 Å
AuthorsLiu, Y.-L. / Zhang, Y. / Oldfield, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA158191 United States
CitationJournal: Biochemistry / Year: 2016
Title: Dynamic Structure and Inhibition of a Malaria Drug Target: Geranylgeranyl Diphosphate Synthase.
Authors: G Ricci, C. / Liu, Y.L. / Zhang, Y. / Wang, Y. / Zhu, W. / Oldfield, E. / McCammon, J.A.
History
DepositionJan 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase, putative
B: Farnesyl pyrophosphate synthase, putative
C: Farnesyl pyrophosphate synthase, putative
D: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,1938
Polymers175,1374
Non-polymers2,0564
Water2,324129
1
A: Farnesyl pyrophosphate synthase, putative
B: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5964
Polymers87,5682
Non-polymers1,0282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-40 kcal/mol
Surface area27240 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase, putative
D: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5964
Polymers87,5682
Non-polymers1,0282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-45 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.447, 108.616, 140.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Farnesyl pyrophosphate synthase, putative


Mass: 43784.188 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Strain: Salvador I / Gene: PVX_092040 / Plasmid: P15-TEV-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5K4U6
#2: Chemical
ChemComp-63D / 4-chloro-2-{[3-(decyloxy)-5-hydroxybenzyl]oxy}-5-sulfamoylbenzoic acid


Mass: 514.031 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H32ClNO7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.34 Å3/Da / Density % sol: 47.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100MM TRIS, 200MM LITHIUM SULFATE, 22% PEG 3,350, PH 8.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.693→50 Å / Num. obs: 46114 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 11.16

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LDW

3ldw


Resolution: 2.693→39.961 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 26.45
RfactorNum. reflection% reflection
Rfree0.267 2322 5.09 %
Rwork0.1921 --
obs0.1959 45617 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.03 Å2 / Biso mean: 40.3228 Å2 / Biso min: 12.48 Å2
Refinement stepCycle: final / Resolution: 2.693→39.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11304 0 136 129 11569
Biso mean--59.57 38.87 -
Num. residues----1408

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