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- PDB-5hn9: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 5hn9
TitleCrystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1186
ComponentsFarnesyl pyrophosphate synthase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ALL HELICES / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / membrane / metal ion binding / 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
2-{[3-(decyloxy)benzyl]oxy}-5-nitrobenzoic acid / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLiu, Y.-L. / Zhang, Y. / OIdfield, 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)176,8558
Polymers175,1374
Non-polymers1,7184
Water7,314406
1
A: Farnesyl pyrophosphate synthase, putative
B: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4274
Polymers87,5682
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
ΔGint-50 kcal/mol
Surface area27320 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase, putative
D: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4274
Polymers87,5682
Non-polymers8592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6370 Å2
ΔGint-49 kcal/mol
Surface area26770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.920, 108.294, 139.866
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-04W / 2-{[3-(decyloxy)benzyl]oxy}-5-nitrobenzoic acid / BPH-1186


Mass: 429.506 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H31NO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THEY HAVE DETERMINED THE CONTENT OF THE GENE BY DNA SEQUENCING

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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: 2.31 Å3/Da / Density % sol: 46.79 %
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: Dec 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 91912 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 7.5 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.581 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MYS

3mys
PDB Unreleased entry


Resolution: 2.12→47.94 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.907 / SU B: 11.192 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4595 5 %RANDOM
Rwork0.177 ---
obs0.18 91598 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.12→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11136 0 124 406 11666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211487
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8821.96515542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.96851365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6724.944538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.924151942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571530
X-RAY DIFFRACTIONr_chiral_restr0.0760.21736
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.028574
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9981.56882
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.295211049
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.32634605
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.8544.54493
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.039311349
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 294 -
Rwork0.17 5341 -
obs--83.25 %

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