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- PDB-2azl: Crystal structure for the mutant F117E of Thermotoga maritima oct... -

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Basic information

Entry
Database: PDB / ID: 2azl
TitleCrystal structure for the mutant F117E of Thermotoga maritima octaprenyl pyrophosphate synthase
Componentsoctoprenyl-diphosphate synthase
KeywordsTRANSFERASE / OPPs / octaprenyl pyrophosphate synthase / Octaprenyl-diphosphate synthase / trans-prenyltransferase / isoprenyl pyrophosphate synthase
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 / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsSun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H.
CitationJournal: J.Bacteriol. / Year: 2005
Title: Homodimeric hexaprenyl pyrophosphate synthase from the thermoacidophilic crenarchaeon Sulfolobus solfataricus displays asymmetric subunit structures
Authors: Sun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H.
History
DepositionSep 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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)33,8821
Polymers33,8821
Non-polymers00
Water5,170287
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: octoprenyl-diphosphate synthase

A: octoprenyl-diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)67,7652
Polymers67,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_557x,-y,-z+21
Buried area3360 Å2
ΔGint-23 kcal/mol
Surface area24960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)151.514, 151.514, 64.606
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-303-

HOH

21A-332-

HOH

31A-504-

HOH

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Components

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


Mass: 33882.277 Da / Num. of mol.: 1 / Mutation: F117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET-32Xa/LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 15644283, UniProt: Q9X1M1*PLUS, EC: 2.5.1.11
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Na+HEPES, Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2005 / Details: mirrors
RadiationMonochromator: MIRRORS / 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. obs: 9443 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 76.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 27.5
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 4.2 / Num. unique all: 2166 / Rsym value: 0.526 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1V4E

1v4e


Resolution: 2.8→35.23 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 511274.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 488 5.3 %RANDOM
Rwork0.223 ---
obs0.223 9215 96.4 %-
all-8732 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9833 Å2 / ksol: 0.328422 e/Å3
Displacement parametersBiso mean: 58 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2---1.58 Å20 Å2
3---3.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 0 287 2502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 64 4.5 %
Rwork0.304 1358 -
obs-892 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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