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- PDB-1zw5: X-ray structure of Farnesyl diphosphate synthase protein -

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Basic information

Entry
Database: PDB / ID: 1zw5
TitleX-ray structure of Farnesyl diphosphate synthase protein
Componentsfarnesyl diphosphate synthase
KeywordsTRANSFERASE / ISOPRENOID PATHWAY / CHOLESTEROL SYNTHESIS / BISPHOSPHONATE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKavanagh, K.L. / Guo, K. / Wu, X. / von Delft, F. / Arrowsmith, C. / Sundstrom, M. / Edwards, A. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.
Authors: Kavanagh, K.L. / Guo, K. / Dunford, J.E. / Wu, X. / Knapp, S. / Ebetino, F.H. / Rogers, M.J. / Russell, R.G. / Oppermann, U.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3May 22, 2013Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Aug 23, 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_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_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_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_conn.ptnr2_label_seq_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 diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3626
Polymers40,7701
Non-polymers5915
Water1,08160
1
A: farnesyl diphosphate synthase
hetero molecules

A: farnesyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,72312
Polymers81,5412
Non-polymers1,18210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7180 Å2
ΔGint-71 kcal/mol
Surface area25900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)112.255, 112.255, 63.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein farnesyl diphosphate synthase / farnesyl pyrophosphate synthetase / dimethylallyl transferase / geranyl transferase / FPPS / FDPS


Mass: 40770.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS / Plasmid: PET11 DERIVATIVE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-ZOL / ZOLEDRONIC ACID / (1-HYDROXY-2-IMIDAZOL-1-YLETHYLIDENE)DIPHOSPHONIC ACID / Zoledronic acid


Mass: 272.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O7P2 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 14% PEG 6000, 0.7 M LiCl, 70 mM citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.984 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2005
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→63 Å / Num. all: 18323 / Num. obs: 17517 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.11 / Net I/σ(I): 13.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.7 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1YV5

1yv5


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.179 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.295 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22311 886 5.1 %RANDOM
Rwork0.17249 ---
all0.17508 17553 --
obs0.17508 16605 94.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.785 Å2
Baniso -1Baniso -2Baniso -3
1--3.86 Å20 Å20 Å2
2---3.86 Å20 Å2
3---7.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 33 60 2790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222801
X-RAY DIFFRACTIONr_bond_other_d0.0010.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9793793
X-RAY DIFFRACTIONr_angle_other_deg0.8435865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.535339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94724.47132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6415467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.521515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.2110.2652
X-RAY DIFFRACTIONr_nbd_other0.1720.22463
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21380
X-RAY DIFFRACTIONr_nbtor_other0.0870.21475
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.130.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2390.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.42731870
X-RAY DIFFRACTIONr_mcbond_other0.6483687
X-RAY DIFFRACTIONr_mcangle_it3.52952715
X-RAY DIFFRACTIONr_scbond_it5.87371244
X-RAY DIFFRACTIONr_scangle_it7.394111077
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 67 -
Rwork0.242 1228 -
obs--97.88 %
Refinement TLS params.Method: refined / Origin x: 9.3239 Å / Origin y: 30.1888 Å / Origin z: -6.7934 Å
111213212223313233
T-0.1421 Å20.0017 Å2-0.0201 Å2--0.0701 Å20.0631 Å2---0.1438 Å2
L3.6652 °20.0684 °2-0.2487 °2-0.9623 °2-0.0095 °2--0.8333 °2
S0.0141 Å °0.3846 Å °0.5119 Å °0.0351 Å °0.0725 Å °0.3939 Å °-0.032 Å °-0.2254 Å °-0.0866 Å °

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