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- PDB-2azj: Crystal structure for the mutant D81C of Sulfolobus solfataricus ... -

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Basic information

Entry
Database: PDB / ID: 2azj
TitleCrystal structure for the mutant D81C of Sulfolobus solfataricus hexaprenyl pyrophosphate synthase
ComponentsGeranylgeranyl pyrophosphate synthetase
KeywordsTRANSFERASE / HexPPs / trans-prenyltransferase
Function / homology
Function and homology information


hexaprenyl diphosphate synthase [geranylgeranyl-diphosphate specific] / hexaprenyl diphosphate synthase (geranylgeranyl-diphosphate specific) activity / prenyltransferase activity / isoprenoid biosynthetic process / metal ion binding
Similarity search - Function
: / 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
: / Hexaprenyl pyrophosphate synthase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsSun, H.Y. / Ko, T.P. / Kuo, C.J. / Guo, R.T. / Chou, C.C. / Liang, P.H. / Wang, A.H.J.
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.J.
History
DepositionSep 11, 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: 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 2.1May 29, 2024Group: Advisory / Data collection / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Geranylgeranyl pyrophosphate synthetase
B: Geranylgeranyl pyrophosphate synthetase


Theoretical massNumber of molelcules
Total (without water)66,6642
Polymers66,6642
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-28 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.926, 91.926, 121.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-282-

HOH

21B-283-

HOH

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Components

#1: Protein Geranylgeranyl pyrophosphate synthetase / Hexaprenyl pyrophosphate synthase


Mass: 33332.016 Da / Num. of mol.: 2 / Mutation: D81C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: gdS-2 / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 15899101, UniProt: Q97W92*PLUS, dimethylallyltranstransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, lithium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 23556 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 33.1 Å2 / Rsym value: 0.049 / Net I/σ(I): 27.4
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.7 / Num. unique all: 2341 / Rsym value: 0.52 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→48.37 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 26602820.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.347 1120 4.8 %RANDOM
Rwork0.317 ---
obs0.317 23211 97.3 %-
all-24221 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.3581 Å2 / ksol: 0.305145 e/Å3
Displacement parametersBiso mean: 55.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å22.26 Å20 Å2
2--0.55 Å20 Å2
3----1.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4460 0 0 393 4853
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.411.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 155 4.2 %
Rwork0.399 3540 -
obs--94 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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