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- PDB-3emc: Crystal structure of XynB, an intracellular xylanase from Paeniba... -

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Basic information

Entry
Database: PDB / ID: 3emc
TitleCrystal structure of XynB, an intracellular xylanase from Paenibacillus barcinonensis
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / (a/b)8 barrel / Glycosidase / Xylan degradation
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
Endo-1,4-beta-xylanase B
Similarity search - Component
Biological speciesBacillus sp. BP-23 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSanz-Aparicio, J. / Isorna, P. / Gonzalez, B.
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 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7123
Polymers38,4761
Non-polymers2362
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.930, 79.110, 91.430
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.06 Å3/Da / Density % sol: 40.42 % / Mosaicity: 0.975 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 35% (v/v) MPD, 17% (w/v) PEG 3350, 100mM tris, 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: Oct 25, 2007 / Details: 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→20 Å / Num. all: 21695 / Num. obs: 20647 / % possible obs: 97.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.023 / Net I/σ(I): 9.922
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.469 / Num. unique all: 1737 / Χ2: 0.809 / % possible all: 80

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.54 / Cor.coef. Fo:Fc: 0.331
Highest resolutionLowest resolution
Rotation3 Å19.94 Å
Translation3 Å19.94 Å

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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: 1HIZ

1hiz


Resolution: 2.1→19.94 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1314 6.8 %random
Rwork0.186 ---
all0.196 19174 --
obs0.186 19174 99.6 %-
Solvent computationBsol: 66.409 Å2
Displacement parametersBiso max: 60.44 Å2 / Biso mean: 15.577 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---3.735 Å20 Å2
3---1.606 Å2
Refine analyzeLuzzati coordinate error obs: 0.075 Å / Luzzati d res low obs: 8 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 16 276 3006
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3161.5
X-RAY DIFFRACTIONc_scbond_it2.0132
X-RAY DIFFRACTIONc_mcangle_it1.9892
X-RAY DIFFRACTIONc_scangle_it2.8422.5
LS refinement shellResolution: 2.1→2.13 Å /
RfactorNum. reflection
Rfree0.32 52
Rwork0.26 -
obs-692
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3mpd.param

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