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- PDB-1wl3: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -

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Basic information

Entry
Database: PDB / ID: 1wl3
TitleCrystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima R91A 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: 3.5 Å
AuthorsGuo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J.
Citation
Journal: To be Published
Title: Biochemical and Structural Basis for Octaprenyl Pyrophosphate Synthase
Authors: Guo, R.T. / Kuo, C.J. / Cheng, Y.S. / Cheng, Y.L. / Liang, P.H. / Wang, A.H.-J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from Thermotoga maritima and Escherichia coli
Authors: Guo, R.T. / Ko, T.P. / Chou, C.C. / Shr, H.L. / Chu, H.M. / Tsai, Y.H. / Liang, P.H. / Wang, A.H.-J.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima and Mechanism of Product Chain Length Determination
Authors: Guo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J.
#3: Journal: 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
DepositionJun 18, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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)67,6282
Polymers67,6282
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-26 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.548, 149.548, 68.031
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-342-

HOH

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Components

#1: Protein octoprenyl-diphosphate synthase / Octaprenyl Pyrophosphate Synthase


Mass: 33814.223 Da / Num. of mol.: 2 / Mutation: R91A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / 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.: 128 / 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: Tris-HCl, NaCl, HEPES, Lithium Sulfate, 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: Feb 15, 2004 / 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: 3.5→50 Å / Num. all: 10209 / Num. obs: 10209 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 10.02 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 16.46
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 3.57 / % possible all: 99.9

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Processing

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

1v4e


Resolution: 3.5→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2959 423 -RANDOM
Rwork0.264 ---
all-10209 --
obs-7993 78.3 %-
Displacement parametersBiso mean: 55.86 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å / Luzzati sigma a obs: 0.76 Å
Refinement stepCycle: LAST / Resolution: 3.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 0 128 4533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0044
X-RAY DIFFRACTIONc_angle_deg1.12
LS refinement shellResolution: 3.5→3.63 Å
RfactorNum. reflection% reflection
Rfree0.4722 32 -
Rwork0.3331 --
obs-528 53.12 %

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