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- PDB-4ryp: Crystal Structure of T. Brucei Farnesyl Diphosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 4ryp
TitleCrystal Structure of T. Brucei Farnesyl Diphosphate Synthase
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
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 speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsCao, R. / Liu, Y.-L. / Oldfield, E.
CitationJournal: ACS Med Chem Lett / Year: 2015
Title: Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.
Authors: Liu, Y.L. / Cao, R. / Wang, Y. / Oldfield, E.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 synthase
B: Farnesyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)88,9512
Polymers88,9512
Non-polymers00
Water3,171176
1
A: Farnesyl pyrophosphate synthase

A: Farnesyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)88,9512
Polymers88,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6280 Å2
ΔGint-37 kcal/mol
Surface area28580 Å2
MethodPISA
2
B: Farnesyl pyrophosphate synthase

B: Farnesyl pyrophosphate synthase


Theoretical massNumber of molelcules
Total (without water)88,9512
Polymers88,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6480 Å2
ΔGint-36 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.331, 119.439, 62.040
Angle α, β, γ (deg.)90.000, 117.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Farnesyl pyrophosphate synthase


Mass: 44475.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q86C09
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 10% MPD, 0.1 AMMONIUM ACETATE, pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 6, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 42016 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 76.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OGD

2ogd


Resolution: 2.21→29.87 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.937 / SU B: 5.992 / SU ML: 0.151 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 2106 5 %RANDOM
Rwork0.1802 ---
obs0.1834 42013 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.44 Å2 / Biso mean: 51.919 Å2 / Biso min: 26.48 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.21→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 0 176 5771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195706
X-RAY DIFFRACTIONr_bond_other_d0.0010.025385
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9617710
X-RAY DIFFRACTIONr_angle_other_deg0.859312380
X-RAY DIFFRACTIONr_chiral_restr0.090.2857
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026379
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
X-RAY DIFFRACTIONr_mcbond_it4.344.9292785
X-RAY DIFFRACTIONr_mcbond_other4.3264.9272784
X-RAY DIFFRACTIONr_mcangle_it6.0627.3573469
LS refinement shellResolution: 2.208→2.265 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 105 -
Rwork0.228 2229 -
all-2334 -
obs--73.63 %

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