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- PDB-1vg6: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -

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Basic information

Entry
Database: PDB / ID: 1vg6
TitleCrystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima F132A/L128A/I123A 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: 3.35 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: Derived calculations / 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


Theoretical massNumber of molelcules
Total (without water)33,7401
Polymers33,7401
Non-polymers00
Water5,477304
1
A: octoprenyl-diphosphate synthase

A: octoprenyl-diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)67,4802
Polymers67,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557-y,-x,-z+21
2
A: octoprenyl-diphosphate synthase

A: octoprenyl-diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)67,4802
Polymers67,4802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x,-y,-z+21
Buried area3430 Å2
ΔGint-25 kcal/mol
Surface area25320 Å2
MethodPISA
3
A: octoprenyl-diphosphate synthase
x 8


Theoretical massNumber of molelcules
Total (without water)269,9218
Polymers269,9218
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_557-x,y,-z+21
crystal symmetry operation6_557x,-y,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_557-y,-x,-z+21
MethodPQS
Unit cell
Length a, b, c (Å)151.969, 151.969, 64.243
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-310-

HOH

21A-382-

HOH

31A-418-

HOH

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Components

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


Mass: 33740.078 Da / Num. of mol.: 1 / Mutation: F132A/L128A/I123A
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 / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 22, 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: 3.35→50 Å / Num. all: 5673 / Num. obs: 5051 / % possible obs: 89 % / Redundancy: 5.65 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.51
Reflection shellResolution: 3.35→3.47 Å / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.17 / Num. unique all: 479 / % possible all: 87.7

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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: 3.35→35.24 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 214 -RANDOM
Rwork0.2407 ---
all-5673 --
obs-3963 69.9 %-
Displacement parametersBiso mean: 48.2 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 3.35→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 0 304 2509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0031
X-RAY DIFFRACTIONc_angle_deg0.72
LS refinement shellResolution: 3.35→3.47 Å
RfactorNum. reflection% reflection
Rfree0.3559 13 -
Rwork0.261 --
obs-219 42.5 %

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