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- PDB-3we9: The crystal structure of YisP from Bacillus subtilis subsp. subti... -

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Basic information

Entry
Database: PDB / ID: 3we9
TitleThe crystal structure of YisP from Bacillus subtilis subsp. subtilis strain 168
ComponentsPutative phytoene/squalene synthase YisP
KeywordsTRANSFERASE / Bacillus subtilis YisP / Isoprenoid / Biofilm / DXXXD motif / squalene synthase
Function / homology
Function and homology information


farnesyl diphosphatase / 15-cis-phytoene synthase activity / hydrolase activity
Similarity search - Function
Squalene/phytoene synthase / Squalene/phytoene synthase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Farnesyl diphosphate phosphatase YisP
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.92 Å
AuthorsHu, Y. / Huang, C.H. / Chan, H.C. / Ko, T.P. / Feng, X. / Oldfield, E. / Guo, R.T.
CitationJournal: To be Published
Title: Crystal structure of Bacillus subtilis YisP in complex with a PEG fragment
Authors: Hu, Y. / Huang, C.H. / Chan, H.C. / Ko, T.P. / Feng, X. / Oldfield, E. / Guo, R.T.
History
DepositionJul 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phytoene/squalene synthase YisP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6962
Polymers31,5461
Non-polymers1501
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.966, 77.576, 91.378
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative phytoene/squalene synthase YisP


Mass: 31546.045 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: yisP, yucD, BSU10810 / Plasmid: pET32 Xa/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21trxB (DE3)
References: UniProt: O06728, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS SAY THIS SEQUENCE INCLUDES MATURE PROTEIN OF YISP.

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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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1 M LiCl, 0.1 M Bicine pH 9.0, 18-20%(w/v) polyethylene glycol 6000, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: MX300HE / Detector: CCD / Date: Nov 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.92→25 Å / Num. obs: 24603 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 32.7
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
RESOLVEmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.92→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.233 1156 RANDOM
Rwork0.211 --
obs0.211 23740 -
all-24553 -
Refinement stepCycle: LAST / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 10 219 2235
LS refinement shellResolution: 1.92→1.99 Å /
RfactorNum. reflection
Rfree0.31 113
Rwork0.262 -

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