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- PDB-2p1c: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -

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Basic information

Entry
Database: PDB / ID: 2p1c
TitleT. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-210
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / 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
ACETATE ION / BETA-MERCAPTOETHANOL / Chem-GG3 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCao, R. / Gao, Y. / Oldfield, E.
CitationJournal: Proteins / Year: 2008
Title: Structures of a potent phenylalkyl bisphosphonate inhibitor bound to farnesyl and geranylgeranyl diphosphate synthases.
Authors: Cao, R. / Chen, C.K. / Guo, R.T. / Wang, A.H. / Oldfield, E.
History
DepositionMar 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
B: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,11514
Polymers88,9512
Non-polymers1,16412
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9490 Å2
ΔGint-99 kcal/mol
Surface area26490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.124, 92.124, 177.747
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#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, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 5 types, 318 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GG3 / {1-HYDROXY-3-[METHYL(4-PHENYLBUTYL)AMINO]PROPANE-1,1-DIYL}BIS(PHOSPHONIC ACID)


Mass: 381.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25NO7P2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.45 Å3/Da / Density % sol: 49.73 %
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: 123.2 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 34615 / % possible obs: 95.7 % / Redundancy: 9.1 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.3
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.664 / % possible all: 69.7

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2EWG

2ewg


Resolution: 2.45→29.69 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 110118.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.299 859 3 %RANDOM
Rwork0.266 ---
obs0.266 28696 87.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.4867 Å2 / ksol: 0.306556 e/Å3
Displacement parametersBiso mean: 53.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.21 Å27.64 Å20 Å2
2--9.21 Å20 Å2
3----18.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.45→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5704 0 70 306 6080
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.771.5
X-RAY DIFFRACTIONc_mcangle_it3.972
X-RAY DIFFRACTIONc_scbond_it4.392
X-RAY DIFFRACTIONc_scangle_it5.622.5
LS refinement shellResolution: 2.45→2.54 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.428 55 2.6 %
Rwork0.431 2033 -
obs--64.4 %

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