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- PDB-3ez3: Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate... -

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Basic information

Entry
Database: PDB / ID: 3ez3
TitleCrystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound
ComponentsFarnesyl pyrophosphate synthase, putative
KeywordsLYASE / malaria / farnesyl pyrophosphate synthase diphosphate / structural genomics / Isoprene biosynthesis / Transferase / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ZOLEDRONIC ACID / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.304 Å
AuthorsWernimont, A.K. / Lew, J. / Zhao, Y. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. ...Wernimont, A.K. / Lew, J. / Zhao, Y. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound
Authors: Wernimont, A.K. / Lew, J. / Zhao, Y. / Kozieradzki, I. / Cossar, D. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / Hui, R. / Artz, J.D.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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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)187,62829
Polymers184,8634
Non-polymers2,76525
Water10,106561
1
A: Farnesyl pyrophosphate synthase, putative
B: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,92216
Polymers92,4322
Non-polymers1,49114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-104 kcal/mol
Surface area26520 Å2
MethodPISA
2
C: Farnesyl pyrophosphate synthase, putative
D: Farnesyl pyrophosphate synthase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,70613
Polymers92,4322
Non-polymers1,27411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-107 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.266, 109.696, 139.529
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Farnesyl pyrophosphate synthase, putative


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)
Strain: salvadorI / Gene: PVX_092040 / Plasmid: p15-tev-lic / Production host: Escherichia coli (E. coli) / Strain (production host): dh5a / References: UniProt: A5K4U6

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Non-polymers , 6 types, 586 molecules

#2: Chemical
ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID


Mass: 272.090 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Comment: medication*YM
#3: Chemical
ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THERE IS A DIFFERENCE BETWEEN THE DATABASE SEQUENCE AND THE SEQUENCE THE AUTHORS ...AUTHORS STATE THAT THERE IS A DIFFERENCE BETWEEN THE DATABASE SEQUENCE AND THE SEQUENCE THE AUTHORS GOT FROM CDNA.

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % PEG3350 0.2 M Li2SO4 0.1 M Tris 8.5 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.304→25 Å / Num. all: 72585 / Num. obs: 72515 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.184 / Rsym value: 0.127 / Χ2: 1.074 / Net I/σ(I): 10.667
Reflection shellResolution: 2.304→2.49 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 7173 / Rsym value: 0.689 / Χ2: 0.848 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.51 Å34.46 Å
Translation2.51 Å34.46 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.304→24.43 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.271 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7 / SU B: 14.326 / SU ML: 0.195 / SU R Cruickshank DPI: 0.46 / SU Rfree: 0.302 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.43 / ESU R Free: 0.294 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3633 5 %RANDOM
Rwork0.226 ---
all0.229 75940 --
obs0.229 72250 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.04 Å2 / Biso mean: 24.385 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.304→24.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11546 0 158 561 12265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02212006
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.97116265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11651438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79924.91558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.325152148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6291533
X-RAY DIFFRACTIONr_chiral_restr0.1150.21799
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028846
X-RAY DIFFRACTIONr_nbd_refined0.2150.26183
X-RAY DIFFRACTIONr_nbtor_refined0.3070.28305
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2735
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.27
X-RAY DIFFRACTIONr_mcbond_it0.6611.57323
X-RAY DIFFRACTIONr_mcangle_it1.105211471
X-RAY DIFFRACTIONr_scbond_it1.81935452
X-RAY DIFFRACTIONr_scangle_it2.6484.54778
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 95 -
Rwork0.29 1929 -
all-2024 -
obs-3467 36.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.641-0.2096-0.39951.32530.68891.8813-0.02040.0144-0.12850.0789-0.00320.19250.0748-0.2630.0237-0.12380.00740.0302-0.15370.0295-0.1098-30.1344.6559.942
22.1086-0.1505-0.61140.86330.4471.6826-0.0515-0.38130.17770.20260.1581-0.0676-0.04640.2246-0.1066-0.02250.03180.0033-0.0558-0.0484-0.0958-17.54114.51126.431
31.312-0.02040.05771.44390.51491.83760.02010.08080.2396-0.0341-0.01950.0521-0.3447-0.09-0.0006-0.07690.03740.0293-0.16280.0183-0.1024-23.02519.777-3.122
41.1816-0.7803-0.54761.85150.66391.60320.10710.258-0.0502-0.2091-0.14730.0964-0.0914-0.15750.0403-0.07990.0114-0.0409-0.1007-0.0021-0.1058-22.0563.791-19.626
51.3112-0.34580.43421.4314-0.67572.0281-0.03230.02070.16410.0549-0.0191-0.1909-0.06310.27580.0514-0.14270.0096-0.0346-0.1522-0.0227-0.112629.615-4.6917.328
62.31460.11430.50470.8929-0.3221.6646-0.0123-0.3852-0.1720.12690.09720.07380.1503-0.1899-0.0849-0.04950.0148-0.0217-0.09670.0372-0.091717.887-14.90623.331
71.2909-0.18190.02711.672-0.51831.74950.03250.0716-0.2376-0.0608-0.0246-0.06020.37130.1288-0.0079-0.0490.0385-0.036-0.1729-0.0208-0.108722.94-19.628-5.311
81.2811-0.8550.69791.7111-0.82221.64660.11560.28570.055-0.1974-0.1927-0.08830.16040.21120.0771-0.06150.02650.0487-0.09170.0111-0.101421.892-3.607-22.154
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 96
2X-RAY DIFFRACTION1A102 - 205
3X-RAY DIFFRACTION2A213 - 395
4X-RAY DIFFRACTION3B36 - 95
5X-RAY DIFFRACTION3B102 - 205
6X-RAY DIFFRACTION4B213 - 395
7X-RAY DIFFRACTION5C38 - 95
8X-RAY DIFFRACTION5C103 - 205
9X-RAY DIFFRACTION6C213 - 350
10X-RAY DIFFRACTION6C360 - 393
11X-RAY DIFFRACTION7D38 - 95
12X-RAY DIFFRACTION7D102 - 205
13X-RAY DIFFRACTION8D213 - 262
14X-RAY DIFFRACTION8D267 - 301
15X-RAY DIFFRACTION8D305 - 395

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