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- PDB-2f7m: Crystal Structure of Unliganded Human FPPS -

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Basic information

Entry
Database: PDB / ID: 2f7m
TitleCrystal Structure of Unliganded Human FPPS
ComponentsFarnesyl Diphosphate Synthase
KeywordsTRANSFERASE / ISOPRENE BIOSYNTHESIS / CHOLESTEROL BIOSYNTHESIS
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / peroxisome / mitochondrial matrix / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol
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
PHOSPHATE ION / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. ...Rondeau, J.-M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W.
CitationJournal: Chemmedchem / Year: 2006
Title: Structural basis for the exceptional in vivo efficacy of bisphosphonate drugs.
Authors: Rondeau, J.M. / Bitsch, F. / Bourgier, E. / Geiser, M. / Hemmig, R. / Kroemer, M. / Lehmann, S. / Ramage, P. / Rieffel, S. / Strauss, A. / Green, J.R. / Jahnke, W.
History
DepositionDec 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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 / 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 / _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

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Assembly

Deposited unit
F: Farnesyl Diphosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2792
Polymers40,1841
Non-polymers951
Water97354
1
F: Farnesyl Diphosphate Synthase
hetero molecules

F: Farnesyl Diphosphate Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5584
Polymers80,3682
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4480 Å2
ΔGint-38 kcal/mol
Surface area29230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.889, 110.889, 76.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE BIOLOGICAL ASSEMBLY IS A HOMODIMER

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Components

#1: Protein Farnesyl Diphosphate Synthase / E.C.2.5.1.1, E.C.2.5.1.10 / FPP synthetase / FPS / Farnesyl pyrophosphate synthetase


Mass: 40183.855 Da / Num. of mol.: 1 / Fragment: Residues 6-353
Source method: isolated from a genetically manipulated source
Details: Includes: Dimethylallyltranstransferase; Geranyltranstransferase
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 TUNER(DE3)
References: UniProt: P14324, dimethylallyltranstransferase, (2E,6E)-farnesyl diphosphate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.2M sodium potassium phosphate, 25% glycerol, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 292.0K

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 15, 2004
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7 Å / Num. all: 21904 / Num. obs: 21795 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.3 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.3
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 8.17 / Num. unique all: 1851 / Num. unique obs: 1795 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPS

1fps


Resolution: 2.3→41.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2643815.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1955 9 %RANDOM
Rwork0.225 ---
all0.228 21795 --
obs0.228 21795 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.656 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso mean: 64 Å2
Baniso -1Baniso -2Baniso -3
1--14.68 Å20 Å20 Å2
2---14.68 Å20 Å2
3---29.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 5 54 2816
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d20.7
X-RAY DIFFRACTIONx_improper_angle_d0.69
X-RAY DIFFRACTIONx_mcbond_it2.071.5
X-RAY DIFFRACTIONx_mcangle_it3.222
X-RAY DIFFRACTIONx_scbond_it3.652
X-RAY DIFFRACTIONx_scangle_it4.942.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 203 5.7 %
Rwork0.283 3367 -
obs-3570 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3water.topwater_rep.param
X-RAY DIFFRACTION4ion.topion.param

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