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- PDB-5cg5: Neutron crystal structure of human farnesyl pyrophosphate synthas... -

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Basic information

Entry
Database: PDB / ID: 5cg5
TitleNeutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBOTOR / prenyl transferase / bisphophonate / osteoprosis / inhibitor / TRANSFERASE-TRANSFERASE INHIBOTOR complex
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
DEUTERATED WATER / Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsYokoyama, T. / Mizuguchi, M. / Ostermann, A. / Kusaka, K. / Niimura, N. / Schrader, T.E. / Tanaka, I.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase
Authors: Yokoyama, T. / Mizuguchi, M. / Ostermann, A. / Kusaka, K. / Niimura, N. / Schrader, T.E. / Tanaka, I.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _citation.journal_id_CSD ..._chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Mar 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / diffrn_detector / diffrn_source / pdbx_struct_conn_angle / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type / _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.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.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
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3875
Polymers41,0311
Non-polymers3564
Water1,910106
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,77410
Polymers82,0622
Non-polymers7128
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6260 Å2
ΔGint-85 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.966, 111.966, 72.754
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 pyrophosphate synthase / Dimethylallyltranstransferase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl ...FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 41030.848 Da / Num. of mol.: 1 / Fragment: UNP residues 74-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Production host: Escherichia coli (E. coli)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: D2O
Nonpolymer detailsAUTHOR STATES THAT THE PYRIDINE NITROGEN FOR THE LIGAND RIS IS IN THE PROTONATED FORM IN THE ...AUTHOR STATES THAT THE PYRIDINE NITROGEN FOR THE LIGAND RIS IS IN THE PROTONATED FORM IN THE CRYSTAL. IN THE DEPOSITED COORDINATES, THE LIGAND RIS HAS TWO DEUTERIUMS, RSD AND D13.

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.5M NaCl, 0.1M acetate buffer

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONPhoton Factory AR-NW12A11
SPALLATION SOURCEJPARC MLF BL-03J-PARC MLF BEAMLINE BL-0323.99
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDNov 17, 2013
CUSTOM-MADE2OSCILLATION CAMERANov 6, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
111
23.991
Reflection
Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Entry-IDRmerge(I) obsDiffraction-ID
1.4-50.078720096.27.15CG50.0621
2.4-53.571841596.23.85CG50.1072
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.4-1.423.20.482195.9
2.4-2.492.70.612298

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data collection
Refinement

Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 1yv5

1yv5

/ Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection allNum. reflection obs% reflection Rfree (%)% reflection obs (%)SU MLDiffraction-IDPhase error
1.402-50.07X-RAY DIFFRACTION0.21830.19360.1948438987160871605.0496.220.29132.35
2.4-53.57NEUTRON DIFFRACTION0.22920.18570.187890218386183864.9198.470.25222.79
Refinement stepCycle: LAST / Resolution: 1.402→50.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 20 106 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066343
X-RAY DIFFRACTIONf_angle_d0.91911277
X-RAY DIFFRACTIONf_dihedral_angle_d18.7821794
X-RAY DIFFRACTIONf_chiral_restr0.139424
X-RAY DIFFRACTIONf_plane_restr0.0041276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.29341330.49082632X-RAY DIFFRACTION93
2.4-2.550.29191650.24882823NEUTRON DIFFRACTION98

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