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- PDB-1v4k: Crystal Structure of Octaprenyl Pyrophosphate Synthase from Hyper... -

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Basic information

Entry
Database: PDB / ID: 1v4k
TitleCrystal Structure of Octaprenyl Pyrophosphate Synthase from Hyperthermophilic Thermotoga maritima S77F 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: 2.45 Å
AuthorsGuo, R.T. / Kuo, C.J. / Chou, C.C. / Ko, T.P. / Shr, H.L. / Liang, P.H. / Wang, A.H.-J.
Citation
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.
#1: Journal: To be Published
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.
History
DepositionNov 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 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 / 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)34,5377
Polymers33,9601
Non-polymers5766
Water6,071337
1
A: octoprenyl-diphosphate synthase
hetero molecules

A: octoprenyl-diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,07414
Polymers67,9212
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_557-y,-x,-z+21
Buried area4370 Å2
ΔGint-167 kcal/mol
Surface area25810 Å2
MethodPISA
2
A: octoprenyl-diphosphate synthase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)276,29456
Polymers271,6838
Non-polymers4,61148
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
Buried area31750 Å2
ΔGint-808 kcal/mol
Surface area89010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.828, 151.828, 64.945
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-1007-

HOH

21A-1017-

HOH

31A-1044-

HOH

41A-1045-

HOH

51A-1257-

HOH

61A-1259-

HOH

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Components

#1: Protein octoprenyl-diphosphate synthase / octaprenyl pyrophosphate synthase


Mass: 33960.434 Da / Num. of mol.: 1 / Mutation: S77F
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.6 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na+Hepes, lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.1 %Triton X-1001drop
30.1 Msodium HEPES1reservoirpH7.5
41.5 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 14277 / Num. obs: 13817 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 8.94 % / Biso Wilson estimate: 43.43 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 35.9
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.9 / % possible all: 82
Reflection
*PLUS
Num. measured all: 123482
Reflection shell
*PLUS
% possible obs: 82 % / Mean I/σ(I) obs: 2.9

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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: 2.45→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.2802 637 -RANDOM
Rwork0.2109 ---
all-14277 --
obs-12263 85.9 %-
Displacement parametersBiso mean: 43.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati sigma a obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 30 337 2575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_angle_deg1.163
LS refinement shellResolution: 2.45→2.54 Å / Rfactor Rfree: 0.2989 / Rfactor Rwork: 0.2316

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