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- PDB-3emz: Crystal structure of xylanase XynB from Paenibacillus barcinonens... -

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Basic information

Entry
Database: PDB / ID: 3emz
TitleCrystal structure of xylanase XynB from Paenibacillus barcinonensis complexed with a conduramine derivative
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / (alpha/beta)8 barrel / GH10 enzyme complex
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cytoplasm
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-HXH / Endo-1,4-beta-xylanase B
Similarity search - Component
Biological speciesBacillus sp. BP-23 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.08 Å
AuthorsSanz-Aparicio, J. / Isorna, P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
Authors: Gallardo, O. / Pastor, F.I. / Polaina, J. / Diaz, P. / Lysek, R. / Vogel, P. / Isorna, P. / Gonzalez, B. / Sanz-Aparicio, J.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8032
Polymers38,4761
Non-polymers3271
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.022, 79.721, 91.183
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 Endo-1,4-beta-xylanase / xylanase


Mass: 38475.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. BP-23 (bacteria) / Gene: xynB / Production host: Escherichia coli (E. coli) / References: UniProt: O69231, endo-1,4-beta-xylanase
#2: Chemical ChemComp-HXH / (1S,2S,3R,6R)-6-[(4-phenoxybenzyl)amino]cyclohex-4-ene-1,2,3-triol


Mass: 327.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.08 Å3/Da / Density % sol: 40.84 % / Mosaicity: 0.524 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 35 % (v/v) MPD, 17 % (w/v), 100mM tris, 10mM inhibitor , VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 30, 2007 / Details: osmic mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 19143 / Num. obs: 20741 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.1 / Χ2: 1.693 / Net I/σ(I): 7.154
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1764 / Χ2: 1.246 / % possible all: 85

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EMC

3emc


Resolution: 2.08→18.85 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.818 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1375 6.6 %random
Rwork0.216 ---
all0.236 20815 --
obs0.23 19023 99.6 %-
Solvent computationBsol: 56.328 Å2
Displacement parametersBiso max: 49.64 Å2 / Biso mean: 14.933 Å2 / Biso min: 3.11 Å2
Baniso -1Baniso -2Baniso -3
1-2.959 Å20 Å20 Å2
2---4.827 Å20 Å2
3---1.868 Å2
Refinement stepCycle: LAST / Resolution: 2.08→18.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 24 268 3007
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.268
X-RAY DIFFRACTIONc_mcbond_it1.1771.5
X-RAY DIFFRACTIONc_scbond_it1.8872
X-RAY DIFFRACTIONc_mcangle_it1.7792
X-RAY DIFFRACTIONc_scangle_it2.6142.5
LS refinement shellResolution: 2.05→2.08 Å
RfactorNum. reflection% reflection
Rfree0.2933 50 -
Rwork0.28 --
obs-725 85 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5rob.paramrob.top

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