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- PDB-3zcd: Native structure of Farnesyl Pyrophosphate Synthase from Pseudomo... -

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Basic information

Entry
Database: PDB / ID: 3zcd
TitleNative structure of Farnesyl Pyrophosphate Synthase from Pseudomonas aeruginosa PA01.
ComponentsGERANYLTRANSTRANSFERASE
KeywordsTRANSFERASE / FPPS
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
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
Geranyltranstransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSchmidberger, J.W. / Schnell, R. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural Characterization of Substrate and Inhibitor Binding to Farnesyl Pyrophosphate Synthase from Pseudomonas Aeruginosa.
Authors: Schmidberger, J.W. / Schnell, R. / Schneider, G.
History
DepositionNov 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)63,1782
Polymers63,1782
Non-polymers00
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-33.7 kcal/mol
Surface area21670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.180, 98.630, 131.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2216-

HOH

21A-2220-

HOH

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Components

#1: Protein GERANYLTRANSTRANSFERASE / / PA4043


Mass: 31588.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9HWY4, (2E,6E)-farnesyl diphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 559 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS AN N-TERMINAL ADDITIONAL SERINE RESULTING FROM CLONING AND CLEAVAGE OF HIS TAG.

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growpH: 6.5
Details: 25% PEG3350, 0.2 M NAF, 0.1 M BISTRISPROPANE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.55→65.54 Å / Num. obs: 78917 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.2
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LJI

3lji


Resolution: 1.55→25.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.601 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20378 3954 5 %RANDOM
Rwork0.15099 ---
obs0.15362 74536 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.379 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å20 Å20 Å2
2--3.78 Å20 Å2
3----2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.55→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 0 559 4654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194190
X-RAY DIFFRACTIONr_bond_other_d0.0050.024087
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9815687
X-RAY DIFFRACTIONr_angle_other_deg1.17639333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92222.963189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4115666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1721546
X-RAY DIFFRACTIONr_chiral_restr0.0940.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214866
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02944
X-RAY DIFFRACTIONr_nbd_refined0.2630.21715
X-RAY DIFFRACTIONr_nbd_other0.2150.23468
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22118
X-RAY DIFFRACTIONr_nbtor_other0.1030.22077
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.297
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0520.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.252
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0590.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr6.7238277
X-RAY DIFFRACTIONr_sphericity_free43.6585151
X-RAY DIFFRACTIONr_sphericity_bonded17.45458620
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 298 -
Rwork0.252 5485 -
obs--99.07 %

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