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- PDB-3ph7: Crystal structure of Plasmodium vivax putative polyprenyl pyropho... -

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Basic information

Entry
Database: PDB / ID: 3ph7
TitleCrystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsLYASE / malaria / farnesyl pyrophosphate synthase diphosphate / Structural Genomics / Structural Genomics Consortium / SGC
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
GERANYLGERANYL DIPHOSPHATE / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWernimont, A.K. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. ...Wernimont, A.K. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular characterization of a novel geranylgeranyl pyrophosphate synthase from Plasmodium parasites.
Authors: Artz, J.D. / Wernimont, A.K. / Dunford, J.E. / Schapira, M. / Dong, A. / Zhao, Y. / Lew, J. / Russell, R.G. / Ebetino, F.H. / Oppermann, U. / Hui, R.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2010ID: 3MYS
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)186,6658
Polymers184,8634
Non-polymers1,8024
Water1,65792
1
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3324
Polymers92,4322
Non-polymers9012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-52 kcal/mol
Surface area27230 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3324
Polymers92,4322
Non-polymers9012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-56 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.095, 108.985, 141.354
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 / Dimethylallyltranstransferase


Mass: 46215.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: PVX_092040 / Plasmid: p15-tev-lic / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5a / References: UniProt: A5K4U6
#2: Chemical
ChemComp-GRG / GERANYLGERANYL DIPHOSPHATE / Geranylgeranyl pyrophosphate


Mass: 450.443 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H36O7P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 44.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% PEG 3350, 0.2 M MgCl2, 1mM GGPP, 2mM MgCl2, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 57810 / Num. obs: 57809 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 66.72 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.05
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 2.81 / Num. unique all: 2848 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→38.19 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9147 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2901 5.03 %RANDOM
Rwork0.2346 ---
all0.2365 57860 --
obs0.2365 57715 99.75 %-
Displacement parametersBiso mean: 68.77 Å2
Baniso -1Baniso -2Baniso -3
1--6.9698 Å20 Å20 Å2
2--2.0822 Å20 Å2
3---4.8876 Å2
Refine analyzeLuzzati coordinate error obs: 0.399 Å
Refinement stepCycle: LAST / Resolution: 2.5→38.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10664 0 114 92 10870
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01109942
X-RAY DIFFRACTIONt_angle_deg1.07149512
X-RAY DIFFRACTIONt_dihedral_angle_d35652
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes2672
X-RAY DIFFRACTIONt_gen_planes15985
X-RAY DIFFRACTIONt_it1088420
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion19.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion15045
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact130964
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2518 214 5.23 %
Rwork0.2387 3874 -
all0.2394 4088 -

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