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- PDB-5k9y: Crystal structure of a thermophilic xylanase A from Bacillus subt... -

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Basic information

Entry
Database: PDB / ID: 5k9y
TitleCrystal structure of a thermophilic xylanase A from Bacillus subtilis 1A1 quadruple mutant Q7H/G13R/S22P/S179C
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / Glycoside Hydrolase Family 11 / Endo-1 / 4-beta-xylanase A / thermostability
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 ...Glycoside hydrolase family 11, active site 2 / Glycosyl hydrolases family 11 (GH11) active site signature 2. / Glycoside hydrolase family 11/12, catalytic domain / Glycoside hydrolase family 11, active site 1 / Glycosyl hydrolases family 11 (GH11) active site signature 1. / Glycoside hydrolase family 11 / Glycosyl hydrolases family 11 (GH11) domain / Glycosyl hydrolases family 11 / Glycosyl hydrolases family 11 (GH11) domain profile. / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsPinheiro, M.P. / Ferreira, T.L. / Silva, S.R.B. / Fuzo, C.A. / Silva, S.R. / Lourenzoni, M.R. / Vieira, D.S. / Ward, R.J. / Nonato, M.C.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)473327/2013 Brazil
Sao Paulo Research Foundation (FAPESP)2007/08703-00 Brazil
CitationJournal: Int. J. Biol. Macromol. / Year: 2017
Title: The role of local residue environmental changes in thermostable mutants of the GH11 xylanase from Bacillus subtilis.
Authors: Silva, S.B. / Pinheiro, M.P. / Fuzo, C.A. / Silva, S.R. / Ferreira, T.L. / Lourenzoni, M.R. / Nonato, M.C. / Vieira, D.S. / Ward, R.J.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)41,0942
Polymers41,0942
Non-polymers00
Water3,765209
1
B: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)20,5471
Polymers20,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Endo-1,4-beta-xylanase A


Theoretical massNumber of molelcules
Total (without water)20,5471
Polymers20,5471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.178, 52.002, 72.474
Angle α, β, γ (deg.)90.000, 91.280, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer as determined by gel filtration.

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Components

#1: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 20547.240 Da / Num. of mol.: 2 / Fragment: residues 29-213 / Mutation: Q7H, G13R, S22P, S179C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: xynA, BSU18840 / Production host: Escherichia coli (E. coli) / References: UniProt: P18429, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.03 Å3/Da / Density % sol: 39.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES and 0.6 M sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.5497 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2007
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5497 Å / Relative weight: 1
ReflectionResolution: 2.2→42.247 Å / Num. obs: 16886 / % possible obs: 100 % / Redundancy: 3.6 % / Rsym value: 0.09 / Net I/av σ(I): 5.41 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.323.60.1973.51100
2.32-2.463.60.1714.11100
2.46-2.633.60.1444.71100
2.63-2.843.60.1135.91100
2.84-3.113.60.1085.71100
3.11-3.483.70.0926.91100
3.48-4.023.60.0798.21100
4.02-4.923.70.0728.61100
4.92-6.963.60.06210.11100
6.96-42.2473.20.0813.9199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XXN

1xxn


Resolution: 2.2→20.33 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.899 / SU R Cruickshank DPI: 0.4036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.404 / ESU R Free: 0.248
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 895 5.3 %RANDOM
Rwork0.1837 ---
obs0.1871 15950 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 68.2 Å2 / Biso mean: 26.818 Å2 / Biso min: 9.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.2→20.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2909 0 0 209 3118
Biso mean---31.45 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.023061
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.8824205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8335380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17123.147143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8841516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212456
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 63 -
Rwork0.259 1148 -
all-1211 -
obs--100 %

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