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- PDB-1rqi: Active Conformation of Farnesyl Pyrophosphate Synthase Bound to I... -

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Basic information

Entry
Database: PDB / ID: 1rqi
TitleActive Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Dimethylallyl S-Thiolodiphosphate
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / isoprenyl synthase
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / prenyltransferase activity / dimethylallyltranstransferase activity / metal ion binding / cytosol
Similarity search - Function
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
DIPHOSPHATE / DIMETHYLALLYL S-THIOLODIPHOSPHATE / ISOPENTYL PYROPHOSPHATE / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsHosfield, D.J. / Zhang, Y. / Dougan, D.R. / Brooun, A. / Tari, L.W. / Swanson, R.V. / Finn, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for bisphosphonate-mediated inhibition of isoprenoid biosynthesis
Authors: Hosfield, D.J. / Zhang, Y. / Dougan, D.R. / Brooun, A. / Tari, L.W. / Swanson, R.V. / Finn, J.
History
DepositionDec 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight
Revision 2.1Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_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_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_conn.ptnr2_label_seq_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: Geranyltranstransferase
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,87813
Polymers64,5372
Non-polymers1,34011
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-82 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.839, 88.839, 174.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Geranyltranstransferase / / Farnesyl-diphosphate synthase / FPP synthase


Mass: 32268.693 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ISPA, B0421 / Production host: Escherichia coli (E. coli)
References: UniProt: P22939, (2E,6E)-farnesyl diphosphate synthase

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Non-polymers , 5 types, 248 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#4: Chemical ChemComp-IPR / ISOPENTYL PYROPHOSPHATE


Mass: 248.108 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14O7P2
#5: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 298 K / Method: nanoliter sitting drop vapor diffusion / pH: 6
Details: MPEG 2000, HEPES, pH 6, Nanoliter Sitting Drop Vapour Diffusion, temperature 298K
Crystal grow
*PLUS
Method: unknown / Details: Hosfield, D., (2003) J. Struct. Biol., 142, 207.

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 27547 / Num. obs: 26473 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.1 / Net I/σ(I): 15.9
Reflection shellResolution: 2.42→2.51 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.44 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 194920 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 2.67

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→43.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.369 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.461 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25928 1343 5.1 %RANDOM
Rwork0.20318 ---
obs0.20604 25126 100 %-
all-26469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.457 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.42→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4544 0 71 237 4852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214668
X-RAY DIFFRACTIONr_bond_other_d0.0020.024335
X-RAY DIFFRACTIONr_angle_refined_deg1.7421.9916321
X-RAY DIFFRACTIONr_angle_other_deg0.809310061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535596
X-RAY DIFFRACTIONr_chiral_restr0.1160.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025212
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02882
X-RAY DIFFRACTIONr_nbd_refined0.2030.21305
X-RAY DIFFRACTIONr_nbd_other0.2230.25308
X-RAY DIFFRACTIONr_nbtor_other0.0860.22863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2242
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3940.28
X-RAY DIFFRACTIONr_mcbond_it0.4051.52976
X-RAY DIFFRACTIONr_mcangle_it0.79424738
X-RAY DIFFRACTIONr_scbond_it1.3431692
X-RAY DIFFRACTIONr_scangle_it2.3554.51583
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.29 88
Rwork0.24 1752
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6648-0.1037-0.05120.8062-0.07531.1230.00650.02850.0108-0.1037-0.01820.0012-0.0114-0.03660.01180.03250.0002-0.00470.0269-0.00960.031965.766165.060910.6183
20.5136-0.0678-0.15390.44690.07961.05890.0037-0.06940.04880.0376-0.014-0.011-0.04190.03340.01030.0193-0.0093-0.02340.0247-0.01250.056568.112766.942342.5715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 3202 - 300
2X-RAY DIFFRACTION2BB23 - 3203 - 300
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.012
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.742

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