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

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Basic information

Entry
Database: PDB / ID: 1rqj
TitleActive Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate and Risedronate
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / bisphosphonate / 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
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Chem-RIS / Farnesyl diphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Derived calculations / Version format compliance
Revision 1.3May 22, 2013Group: Non-polymer description
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Structure summary
Category: pdbx_distant_solvent_atoms / refine / Item: _chem_comp.pdbx_synonyms / _refine.ls_d_res_low
Revision 1.5Feb 14, 2024Group: 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_struct_conn_angle / refine_hist / struct_conn / 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 / _refine_hist.d_res_low / _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_conn.ptnr2_label_seq_id / _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)65,59912
Polymers64,3952
Non-polymers1,20410
Water7,440413
1
A: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8006
Polymers32,1981
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8006
Polymers32,1981
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Geranyltranstransferase
hetero molecules

B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,59912
Polymers64,3952
Non-polymers1,20410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area6550 Å2
ΔGint-75 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.800, 88.800, 174.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 32197.615 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
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 298 K / Method: nanoliter sitting drop vapor diffusion / pH: 6.5
Details: MPEG 2000, HEPES, pH 6.5, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 52067 / Num. obs: 51703 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.66 % / Rsym value: 0.077 / Net I/σ(I): 27.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.51 / % possible all: 96.2
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 396530 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.645 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23906 2635 5.1 %RANDOM
Rwork0.20558 ---
obs0.20729 49037 99.33 %-
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: 22.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20 Å2
2--0.44 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 68 413 4985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214665
X-RAY DIFFRACTIONr_bond_other_d0.0020.024339
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9916322
X-RAY DIFFRACTIONr_angle_other_deg0.826310079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955595
X-RAY DIFFRACTIONr_chiral_restr0.0740.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025212
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02887
X-RAY DIFFRACTIONr_nbd_refined0.2070.21282
X-RAY DIFFRACTIONr_nbd_other0.2350.25376
X-RAY DIFFRACTIONr_nbtor_other0.0840.22860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2365
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.2137
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2310.235
X-RAY DIFFRACTIONr_mcbond_it0.5451.52971
X-RAY DIFFRACTIONr_mcangle_it1.04224732
X-RAY DIFFRACTIONr_scbond_it1.82331694
X-RAY DIFFRACTIONr_scangle_it3.0724.51590
LS refinement shellResolution: 1.95→1.998 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 193
Rwork0.229 3408
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.23

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