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- PDB-6tj2: Extracellular alpha/beta-hydrolase from Paenibacillus species sha... -

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Basic information

Entry
Database: PDB / ID: 6tj2
TitleExtracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to Tobacco Salicylic Acid Binding Protein 2
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / alpha/beta-hydrolase / methyl salicylate esterase / Paenibacillus / rhizosphere / SABP2 / salicylic acid
Function / homologyAlpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase
Function and homology information
Biological speciesPaenibacillus sp. VTT E-133280 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsFulop, V. / Wilkinson, R.C.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M003523/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/M025772/1 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2.
Authors: Wilkinson, R.C. / Rahman Pour, R. / Jamshidi, S. / Fulop, V. / Bugg, T.D.H.
History
DepositionNov 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
C: Alpha/beta hydrolase


Theoretical massNumber of molelcules
Total (without water)95,3143
Polymers95,3143
Non-polymers00
Water12,016667
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Crystal structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint0 kcal/mol
Surface area27190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.860, 112.430, 126.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha/beta hydrolase


Mass: 31771.234 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. VTT E-133280 (bacteria)
Gene: CA600_10415 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A264DUQ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 1.79 Å3/Da / Density % sol: 31.3 % / Description: Rod
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium fluoride, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2017
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.32→57 Å / Num. obs: 159905 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.025 / Rrim(I) all: 0.064 / Rsym value: 0.059 / Net I/σ(I): 17.7
Reflection shellResolution: 1.32→1.39 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2 / Num. unique obs: 22076 / CC1/2: 0.737 / Rpim(I) all: 0.32 / Rrim(I) all: 0.807 / Rsym value: 0.739 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DQZ

3dqz


Resolution: 1.32→56.22 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.824 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1825 6430 4 %RANDOM
Rwork0.1602 ---
obs0.1611 153475 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.83 Å2 / Biso mean: 15.128 Å2 / Biso min: 8.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.32→56.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5762 0 0 667 6429
Biso mean---26.28 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135938
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175403
X-RAY DIFFRACTIONr_angle_refined_deg1.931.6518063
X-RAY DIFFRACTIONr_angle_other_deg1.5551.57312591
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385729
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27323.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5315970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2221524
X-RAY DIFFRACTIONr_chiral_restr0.110.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021252
LS refinement shellResolution: 1.32→1.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 449 -
Rwork0.291 10113 -
all-10562 -
obs--89.39 %

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