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- PDB-2rah: Human FDPS synthase in complex with novel inhibitor -

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Basic information

Entry
Database: PDB / ID: 2rah
TitleHuman FDPS synthase in complex with novel inhibitor
ComponentsFarnesyl pyrophosphate synthetase
KeywordsTRANSFERASE / mainly alpha / orthogonal bundle / osteoporosis / Cholesterol biosynthesis / Cytoplasm / Host-virus interaction / Isoprene biosynthesis / Lipid synthesis / Steroid biosynthesis / Sterol biosynthesis
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
Chem-11P / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsEvdokimov, A.G. / Barnett, B.L. / Ebetino, F.H. / Pokross, M.
CitationJournal: To be Published
Title: Human FDPS synthase in complex with novel inhibitor
Authors: Evdokimov, A.G. / Barnett, B.L. / Ebetino, F.H. / Pokross, M.
History
DepositionSep 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
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.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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9014
Polymers43,4711
Non-polymers4303
Water2,036113
1
A: Farnesyl pyrophosphate synthetase
hetero molecules

A: Farnesyl pyrophosphate synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8028
Polymers86,9432
Non-polymers8596
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area4670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.171, 111.171, 70.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthetase / FPP synthetase / FPS / Farnesyl diphosphate synthetase


Mass: 43471.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: p11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-11P / [(7R)-6,7-dihydro-5H-cyclopenta[c]pyridin-7-yl(hydroxy)methylene]bis(phosphonic acid)


Mass: 309.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13NO7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 0.2M Ammonium sulfate, 15% isopropanol, 15% ethylene glycol, pH 4.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2005 / Details: mirror/slit
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→35.2 Å / Num. all: 26598 / Num. obs: 26598 / % possible obs: 87.43 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.55
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2360 / % possible all: 57.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
SERGUIdata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementStarting model: 1ZW5

1zw5


Resolution: 2→35.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.73 / SU ML: 0.133 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1355 5.1 %RANDOM
Rwork0.217 ---
all0.22 26558 --
obs0.219 26558 87.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.028 Å2
Baniso -1Baniso -2Baniso -3
1--2.43 Å20 Å20 Å2
2---2.43 Å20 Å2
3---4.86 Å2
Refinement stepCycle: LAST / Resolution: 2→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 25 113 2918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222867
X-RAY DIFFRACTIONr_angle_refined_deg1.1881.983898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.8115348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94724.861144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62415501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2791515
X-RAY DIFFRACTIONr_chiral_restr0.0920.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022181
X-RAY DIFFRACTIONr_nbd_refined0.2430.21382
X-RAY DIFFRACTIONr_nbtor_refined0.3240.22009
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.212
X-RAY DIFFRACTIONr_mcbond_it1.4691.51735
X-RAY DIFFRACTIONr_mcangle_it2.32522752
X-RAY DIFFRACTIONr_scbond_it3.67931272
X-RAY DIFFRACTIONr_scangle_it5.3754.51141
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 66 -
Rwork0.271 1147 -
all-1213 -
obs-2360 54.81 %

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