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- PDB-3dyg: T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphospho... -

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Basic information

Entry
Database: PDB / ID: 3dyg
TitleT. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461
ComponentsFARNESYL PYROPHOSPHATE SYNTHASE
KeywordsTRANSFERASE / PROTEIN-BISPHOSPHONATE COMPLEX / Isoprene biosynthesis
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
ACETATE ION / BETA-MERCAPTOETHANOL / Chem-NI9 / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCao, R. / Gao, Y. / Robinson, H. / Goddard, A. / Oldfield, E.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / ...Authors: Zhang, Y. / Cao, R. / Yin, F. / Hudock, M.P. / Guo, R.T. / Krysiak, K. / Mukherjee, S. / Gao, Y.G. / Robinson, H. / Song, Y. / No, J.H. / Bergan, K. / Leon, A. / Cass, L. / Goddard, A. / Chang, T.K. / Lin, F.Y. / Van Beek, E. / Papapoulos, S. / Wang, A.H. / Kubo, T. / Ochi, M. / Mukkamala, D. / Oldfield, E.
History
DepositionJul 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _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)90,21216
Polymers88,9512
Non-polymers1,26114
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-116 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.565, 118.520, 63.186
Angle α, β, γ (deg.)90.00, 112.36, 90.00
Int Tables number5
Space group name H-MC121

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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 , 6 types, 575 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.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NI9 / 3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM


Mass: 302.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11FNO7P2
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
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: NSLS / Beamline: X8C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 6, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 53536 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 0.101
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.53 / % possible all: 98.3

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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: 2.1→29.22 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 58133.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1533 3 %RANDOM
Rwork0.207 ---
obs0.207 51405 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.43 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å22.89 Å2
2---5.78 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5742 0 58 577 6377
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.24
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.71.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.33 155 2.9 %
Rwork0.258 5192 -
obs--89.8 %

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