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- PDB-1wl2: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -

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Basic information

Entry
Database: PDB / ID: 1wl2
TitleCrystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima R90A 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: 2.8 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: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1985
Polymers33,8141
Non-polymers3844
Water4,774265
1
A: octoprenyl-diphosphate synthase
hetero molecules

A: octoprenyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,39710
Polymers67,6282
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557-y,-x,-z+21
2
A: octoprenyl-diphosphate synthase
hetero molecules

A: octoprenyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,39710
Polymers67,6282
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x,-y,-z+21
Buried area5040 Å2
ΔGint-136 kcal/mol
Surface area24920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)150.861, 150.861, 64.823
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-579-

HOH

21A-604-

HOH

31A-694-

HOH

41A-758-

HOH

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Components

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


Mass: 33814.223 Da / Num. of mol.: 1 / Mutation: R90A
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: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / 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 10, 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: 2.8→50 Å / Num. all: 9507 / Num. obs: 9426 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 7.94 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24.92
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 3.78 / Num. unique all: 917 / % possible all: 100

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Processing

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

1v4e


Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 436 -RANDOM
Rwork0.2328 ---
all-9507 --
obs-8361 87.9 %-
Displacement parametersBiso mean: 46.36 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati sigma a obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 20 265 2496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.003
X-RAY DIFFRACTIONc_angle_deg0.78
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection% reflection
Rfree0.2935 36 -
Rwork0.278 --
obs-644 70.23 %

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