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- PDB-3mav: Crystal structure of Plasmodium vivax putative farnesyl pyrophosp... -

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Basic information

Entry
Database: PDB / ID: 3mav
TitleCrystal structure of Plasmodium vivax putative farnesyl pyrophosphate synthase (Pv092040)
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / PLASMODIUM VIVAX FARNESYL PYROPHOSPHATE SYNTHASE / PV092040 / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Isoprene biosynthesis
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
Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, A. / Dunford, J. / Lew, J. / Wernimont, A.K. / Ren, H. / Zhao, Y. / Koeieradzki, I. / Opperman, U. / Sundstrom, M. / Weigelt, J. ...Dong, A. / Dunford, J. / Lew, J. / Wernimont, A.K. / Ren, H. / Zhao, Y. / Koeieradzki, I. / Opperman, U. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / 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
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionApr 14, 2010ID: 2IHI
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 28, 2021Group: Database references / Derived calculations / Refinement description
Category: refine / struct_ref_seq_dif / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details ..._refine.ls_percent_reflns_obs / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 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
B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,20313
Polymers184,3384
Non-polymers8659
Water6,666370
1
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7458
Polymers92,1692
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-116 kcal/mol
Surface area28200 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,4575
Polymers92,1692
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-86 kcal/mol
Surface area28100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.969, 116.390, 92.416
Angle α, β, γ (deg.)90.00, 116.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Farnesyl pyrophosphate synthase


Mass: 46084.555 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 DERIVED FROM PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 ROSETTA-R3 / References: UniProt: A5K4U6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 22% PEG 3350, 200 MM LI2SO4, 100 MM TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2006 / Details: M
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 92263 / Num. obs: 92263 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 43.16 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.53 / Num. unique all: 4429 / Rsym value: 0.564 / % possible all: 96.6

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
Coot0.5.2model building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YHK

1yhk


Resolution: 2.1→20.99 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1850 2.01 %RANDOM
Rwork0.2285 ---
all0.2291 92263 --
obs0.2291 92136 99.9 %-
Displacement parametersBiso mean: 46.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.151 Å20 Å20.9022 Å2
2--0.1029 Å20 Å2
3----0.2539 Å2
Refine analyzeLuzzati coordinate error obs: 0.337 Å
Refinement stepCycle: LAST / Resolution: 2.1→20.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10961 0 45 370 11376
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.011
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg0.92
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
LS refinement shellResolution: 2.1→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2952 134 2.03 %
Rwork0.2601 6471 -

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