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- PDB-1vg4: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -

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Basic information

Entry
Database: PDB / ID: 1vg4
TitleCrystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima F132A/L128A mutant
Componentsoctoprenyl-diphosphate synthase
KeywordsTRANSFERASE / trans-type prenyltransferase / thermophilic
Function / homology
Function and homology information


prenyltransferase activity / isoprenoid biosynthetic process
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
Octoprenyl-diphosphate synthase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuo, R.T. / Kuo, C.J. / Ko, T.P. / Chou, C.C. / Liang, P.H. / Wang, A.H.-J.
CitationJournal: Biochemistry / Year: 2004
Title: A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products
Authors: Guo, R.T. / Kuo, C.J. / Ko, T.P. / Chou, C.C. / Liang, P.H. / Wang, A.H.-J.
History
DepositionApr 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: octoprenyl-diphosphate synthase
B: octoprenyl-diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)67,5642
Polymers67,5642
Non-polymers00
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-29 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.430, 151.430, 67.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-469-

HOH

21A-478-

HOH

31A-487-

HOH

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Components

#1: Protein octoprenyl-diphosphate synthase / Trans-octaprenyltranstransferase


Mass: 33782.160 Da / Num. of mol.: 2 / Mutation: F132A/L128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET32XA-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9X1M1, EC: 2.5.1.11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.86 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, Lithium sulfate, PEG 900, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 11, 2003 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 12236 / Num. obs: 11660 / % possible obs: 95.1 % / Redundancy: 7.37 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.05
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.75 / Num. unique all: 1086 / % possible all: 91.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4E

1v4e


Resolution: 3.3→47.89 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.321 477 -RANDOM
Rwork0.277 ---
all-12236 --
obs-9013 73.7 %-
Displacement parametersBiso mean: 58.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 3.3→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 0 378 4816
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0041
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shellResolution: 3.3→3.42 Å
RfactorNum. reflection% reflection
Rfree0.326 24 -
Rwork0.274 --
obs-527 46.38 %

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