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- PDB-5hn8: Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 5hn8
TitleCrystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182
ComponentsFarnesyl pyrophosphate synthase, putative
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / 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-HXK / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / diffrn_radiation_wavelength / 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)176,7879
Polymers175,1374
Non-polymers1,6505
Water2,900161
1
A: Farnesyl pyrophosphate synthase, putative
C: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,3454
Polymers87,5682
Non-polymers7772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-48 kcal/mol
Surface area27360 Å2
MethodPISA
2
B: Farnesyl pyrophosphate synthase, putative
D: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4415
Polymers87,5682
Non-polymers8733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-64 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.072, 117.220, 92.786
Angle α, β, γ (deg.)90.000, 116.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 500
2113B1 - 500
3113C1 - 500
4113D1 - 500

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: A5K4U6
#2: Chemical
ChemComp-HXK / 2-{[3-hydroxy-5-(octyloxy)benzyl]sulfanyl}benzoic acid / BPH-1182


Mass: 388.520 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H28O4S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200MM LISO4, 20% PEG3350, 100MM TRIS, PH 8.5, HANGING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 43920 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 9.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.561 / Rejects: 0 / % possible all: 97.5

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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: 3LDW

3ldw


Resolution: 2.7→31.1 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.876 / SU B: 17.849 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.296 2075 5.1 %RANDOM
Rwork0.259 ---
obs0.261 38662 92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 101.19 Å2 / Biso mean: 47.09 Å2 / Biso min: 6.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.21 Å2
2--0.21 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.7→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10497 0 113 161 10771
Biso mean--53.3 32.84 -
Num. residues----1315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02210816
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.96414635
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.70651282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84524.94502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.512151794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5611526
X-RAY DIFFRACTIONr_chiral_restr0.1050.21647
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028038
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_it0.9281.56517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.95210423
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scbond_it3.00534299
X-RAY DIFFRACTIONSIDE-CHAIN BOND OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scangle_it5.3074.54212
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B REFINED ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1200TIGHT POSITIONAL0.060.05
B1200TIGHT POSITIONAL0.050.05
C1200TIGHT POSITIONAL0.060.05
D1200TIGHT POSITIONAL0.050.05
A1164LOOSE POSITIONAL0.075
B1164LOOSE POSITIONAL0.055
C1164LOOSE POSITIONAL0.065
D1164LOOSE POSITIONAL0.055
A1200TIGHT THERMAL0.130.5
B1200TIGHT THERMAL0.10.5
C1200TIGHT THERMAL0.120.5
D1200TIGHT THERMAL0.110.5
A1164LOOSE THERMAL0.1410
B1164LOOSE THERMAL0.110
C1164LOOSE THERMAL0.1210
D1164LOOSE THERMAL0.1110
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 155 -
Rwork0.316 2346 -
all-2501 -
obs--76.58 %

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