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- PDB-3wjn: Crystal structure of Octaprenyl Pyrophosphate synthase from Esche... -

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Basic information

Entry
Database: PDB / ID: 3wjn
TitleCrystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli with farnesyl S-thiol-pyrophosphate (FSPP)
ComponentsOctaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / site-directed mutagenesis / product chain length
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / Chem-FPS / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHan, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. ...Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Oldfield, E. / Liang, P.H. / Guo, R.T. / Ma, Y.H.
CitationJournal: Proteins / Year: 2015
Title: Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from Escherichia coli reveal the catalytic and chain-length determining mechanisms.
Authors: Han, X. / Chen, C.C. / Kuo, C.J. / Huang, C.H. / Zheng, Y. / Ko, T.P. / Zhu, Z. / Feng, X. / Wang, K. / Oldfield, E. / Wang, A.H. / Liang, P.H. / Guo, R.T. / Ma, Y.
History
DepositionOct 12, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _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 1.2Nov 8, 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: Octaprenyl diphosphate synthase
B: Octaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3383
Polymers73,9392
Non-polymers3981
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-35 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.742, 128.239, 46.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Octaprenyl diphosphate synthase / Octaprenyl Pyrophosphate synthase


Mass: 36969.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O104:H4 str. 2009EL-2071 / Gene: O3O_22640 / Plasmid: pET46a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K0BUH0, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.3M Magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.5, 24% w/v polyethylene glycol 3350 , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 22242 / % possible obs: 99.8 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 24
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.454 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WJK

3wjk


Resolution: 2.6→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2687 1051 4.7 %RANDOM
Rwork0.2184 20466 --
obs-21517 96.8 %-
Solvent computationBsol: 22.1852 Å2
Displacement parametersBiso mean: 55.0101 Å2
Baniso -1Baniso -2Baniso -3
1-18.361 Å20 Å20 Å2
2---11.867 Å20 Å2
3----6.494 Å2
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 24 153 4823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3291.5
X-RAY DIFFRACTIONc_scbond_it2.0522
X-RAY DIFFRACTIONc_mcangle_it2.2612
X-RAY DIFFRACTIONc_scangle_it3.1652.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree: 0.35 / Rfactor Rwork: 0.302
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2fspp-RT.param
X-RAY DIFFRACTION3water_rep.param

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