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- PDB-1vg2: Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyper... -

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Basic information

Entry
Database: PDB / ID: 1vg2
TitleCrystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima A76Y 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: 3.1 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 2.0Nov 10, 2021Group: Atomic model / Database references / Category: atom_site / database_2 / struct_ref_seq_dif
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / pdbx_validate_symm_contact

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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)33,9921
Polymers33,9921
Non-polymers00
Water4,648258
1
A: octoprenyl-diphosphate synthase

A: octoprenyl-diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)67,9852
Polymers67,9852
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)67,9852
Polymers67,9852
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 area24860 Å2
MethodPISA
3
A: octoprenyl-diphosphate synthase
x 8


Theoretical massNumber of molelcules
Total (without water)271,9398
Polymers271,9398
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)151.392, 151.392, 64.869
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-520-

HOH

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Components

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


Mass: 33992.434 Da / Num. of mol.: 1 / Mutation: A76Y
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.: 258 / 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: Jul 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: 3.1→50 Å / Num. all: 7117 / Num. obs: 7104 / % possible obs: 99.8 % / Redundancy: 10 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 34.89
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 4.95 / Num. unique all: 689 / % possible all: 100

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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: 3.1→47.87 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 343 -RANDOM
Rwork0.2443 ---
all-7117 --
obs-6180 86.8 %-
Displacement parametersBiso mean: 55.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å / Luzzati sigma a obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 3.1→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 0 258 2491
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0032
X-RAY DIFFRACTIONc_angle_deg0.81
LS refinement shellResolution: 3.1→3.21 Å
RfactorNum. reflection% reflection
Rfree0.3252 25 -
Rwork0.3126 --
obs-424 65.17 %

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