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- PDB-1fps: CRYSTAL STRUCTURE OF RECOMBINANT FARNESYL DIPHOSPHATE SYNTHASE AT... -

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Basic information

Entry
Database: PDB / ID: 1fps
TitleCRYSTAL STRUCTURE OF RECOMBINANT FARNESYL DIPHOSPHATE SYNTHASE AT 2.6 ANGSTROMS RESOLUTION
ComponentsFARNESYL DIPHOSPHATE SYNTHASE
KeywordsPRENYLTRANSFERASE
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 2. / Polyprenyl synthases signature 1. / 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
Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsTarshis, L.C. / Yan, M. / Poulter, C.D. / Sacchettini, J.C.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of recombinant farnesyl diphosphate synthase at 2.6-A resolution.
Authors: Tarshis, L.C. / Yan, M. / Poulter, C.D. / Sacchettini, J.C.
History
DepositionJun 30, 1994Processing site: BNL
Revision 1.0Jul 10, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FARNESYL DIPHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)40,0211
Polymers40,0211
Non-polymers00
Water1,42379
1
A: FARNESYL DIPHOSPHATE SYNTHASE

A: FARNESYL DIPHOSPHATE SYNTHASE


Theoretical massNumber of molelcules
Total (without water)80,0412
Polymers80,0412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area4340 Å2
ΔGint-31 kcal/mol
Surface area31080 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.600, 88.600, 276.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein FARNESYL DIPHOSPHATE SYNTHASE


Mass: 40020.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken)
References: UniProt: P08836, (2E,6E)-farnesyl diphosphate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.65 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme1drop
20.78 Mtartrate1reservoir
30.1 MHEPES1reservoir
420 mMphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.16 Å / Num. obs: 25159 / % possible obs: 80.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.115

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.194 -
obs0.194 13222
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2815 0 0 79 2894
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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