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- PDB-3ryw: Crystal structure of P. vivax geranylgeranyl diphosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 3ryw
TitleCrystal structure of P. vivax geranylgeranyl diphosphate synthase complexed with BPH-811
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / geranylgeranyl diphosphate synthase / BPH-811
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
Chem-K9H / Farnesyl pyrophosphate synthase, putative
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsNo, J.H. / Liu, Y.-L. / Zhang, Y. / Oldfield, E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Lipophilic analogs of zoledronate and risedronate inhibit Plasmodium geranylgeranyl diphosphate synthase (GGPPS) and exhibit potent antimalarial activity.
Authors: No, J.H. / de Macedo Dossin, F. / Zhang, Y. / Liu, Y.L. / Zhu, W. / Feng, X. / Yoo, J.A. / Lee, E. / Wang, K. / Hui, R. / Freitas-Junior, L.H. / Oldfield, E.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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
B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,23224
Polymers184,8634
Non-polymers2,36920
Water1,27971
1
A: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,61612
Polymers92,4322
Non-polymers1,18510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-150 kcal/mol
Surface area27820 Å2
MethodPISA
2
B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,61612
Polymers92,4322
Non-polymers1,18510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10070 Å2
ΔGint-147 kcal/mol
Surface area28310 Å2
MethodPISA
3
A: Farnesyl pyrophosphate synthase
D: Farnesyl pyrophosphate synthase
hetero molecules

B: Farnesyl pyrophosphate synthase
C: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,23224
Polymers184,8634
Non-polymers2,36920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area23250 Å2
ΔGint-309 kcal/mol
Surface area53160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.744, 106.582, 139.031
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


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: Salvador I / Gene: ggpps, PVX_092040 / Production host: Escherichia coli (E. coli) / References: UniProt: A5K4U6
#2: Chemical
ChemComp-K9H / {2-[5-(decyloxy)pyridin-3-yl]ethane-1,1-diyl}bis(phosphonic acid)


Mass: 423.378 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H31NO7P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 38.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% PEG 3350, 1mM BPH-811, 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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 5, 2010
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 37105 / Num. obs: 36585 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.141
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.05 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3CC9

3cc9


Resolution: 2.9→35.22 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 18.411 / SU ML: 0.349 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25957 1649 5 %RANDOM
Rwork0.20773 ---
obs0.21033 31290 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.868 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11563 0 140 71 11774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211920
X-RAY DIFFRACTIONr_bond_other_d0.0050.027896
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.96716118
X-RAY DIFFRACTIONr_angle_other_deg1.263.00219195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51851414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08425.009553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.275152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2591530
X-RAY DIFFRACTIONr_chiral_restr0.0740.21801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212967
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022403
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_it0.7731.57113
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.513211480
X-RAY DIFFRACTIONr_scbond_it2.18834875
X-RAY DIFFRACTIONr_scangle_it3.6634.54722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 108 -
Rwork0.283 2127 -
obs--98.76 %

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