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- PDB-1rtr: Crystal Structure of S. Aureus Farnesyl Pyrophosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 1rtr
TitleCrystal Structure of S. Aureus Farnesyl Pyrophosphate Synthase
Componentsgeranyltranstransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / transferase activity / cytoplasm
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
IspA protein / IspA protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsHosfield, D.J. / Zhang, Y. / Dougan, D.R. / Brooun, A. / Tari, L.W. / Swanson, R.V. / Finn, J.
CitationJournal: J.Mol.Biol. / 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 10, 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 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: geranyltranstransferase
B: geranyltranstransferase


Theoretical massNumber of molelcules
Total (without water)67,7232
Polymers67,7232
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-52 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.201, 150.201, 163.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein geranyltranstransferase / Farnesyl Pyrophosphate Synthase


Mass: 33861.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NWD6, UniProt: A0A0H3JWH0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 298 K / Method: nanoliter sitting drop vapor diffusion / pH: 5
Details: PEG 1000, Phosphate, pH 5, Nanoliter Sitting Drop Vapour Diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 39253 / Num. obs: 38076 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.042 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.65 Å / % possible all: 0.93

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.4 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26573 3779 9.9 %RANDOM
Rwork0.22232 ---
obs0.22662 34204 99.96 %-
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: 61.818 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4301 0 0 161 4462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214358
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9775886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8115544
X-RAY DIFFRACTIONr_chiral_restr0.0960.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023178
X-RAY DIFFRACTIONr_nbd_refined0.2160.22189
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2152
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.212
X-RAY DIFFRACTIONr_mcbond_it0.571.52714
X-RAY DIFFRACTIONr_mcangle_it1.11624367
X-RAY DIFFRACTIONr_scbond_it1.58731644
X-RAY DIFFRACTIONr_scangle_it2.8014.51519
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 278
Rwork0.349 2413

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