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- PDB-2cov: Crystal structure of CBM31 from beta-1,3-xylanase -

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Basic information

Entry
Database: PDB / ID: 2cov
TitleCrystal structure of CBM31 from beta-1,3-xylanase
Componentsbeta-1,3-xylanase
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding module / family 31 CBM / beta-1 / 3-xylanase
Function / homology
Function and homology information


xylan 1,3-beta-xylosidase activity / endo-1,3-beta-xylanase / xylan endo-1,3-beta-xylosidase activity / substituted mannan metabolic process / mannan endo-1,4-beta-mannosidase activity / polysaccharide binding / xylan catabolic process / cellulose catabolic process
Similarity search - Function
Beta-1,3-xylanase, CBM31 domain / Beta-1,3-xylanase / Beta-1,3-xylanase, CBM31 domain superfamily / Family 31 carbohydrate binding protein / Glycoside hydrolase family 26 / Glycosyl hydrolase family 26 domain / Glycosyl hydrolases family 26 (GH26) domain profile. / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesAlcaligenes sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.25 Å
AuthorsHashimoto, H. / Tamai, Y. / Okazaki, F. / Tamaru, Y. / Shimizu, T. / Araki, T. / Sato, M.
CitationJournal: Febs Lett. / Year: 2005
Title: The first crystal structure of a family 31 carbohydrate-binding module with affinity to beta-1,3-xylan
Authors: Hashimoto, H. / Tamai, Y. / Okazaki, F. / Tamaru, Y. / Shimizu, T. / Araki, T. / Sato, M.
History
DepositionMay 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: beta-1,3-xylanase
E: beta-1,3-xylanase
F: beta-1,3-xylanase
G: beta-1,3-xylanase
H: beta-1,3-xylanase
I: beta-1,3-xylanase


Theoretical massNumber of molelcules
Total (without water)72,9326
Polymers72,9326
Non-polymers00
Water10,287571
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.551, 78.290, 111.420
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
beta-1,3-xylanase


Mass: 12155.296 Da / Num. of mol.: 6 / Fragment: carbohydrate-binding module, residues 378-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes sp. (bacteria) / Strain: XY-234 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RS40
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 153374 / % possible obs: 95.4 %

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.25→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.413 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17522 7695 5 %RANDOM
Rwork0.14935 ---
obs0.15067 145607 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.097 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---0.6 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 0 571 4937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224433
X-RAY DIFFRACTIONr_bond_other_d0.0010.023605
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.9096019
X-RAY DIFFRACTIONr_angle_other_deg0.90538393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.335526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20325.154260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05215674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7811518
X-RAY DIFFRACTIONr_chiral_restr0.1260.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02986
X-RAY DIFFRACTIONr_nbd_refined0.2080.2651
X-RAY DIFFRACTIONr_nbd_other0.1940.23708
X-RAY DIFFRACTIONr_nbtor_refined0.1920.22212
X-RAY DIFFRACTIONr_nbtor_other0.0910.22734
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2393
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1620.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5771.53446
X-RAY DIFFRACTIONr_mcbond_other1.0571.51110
X-RAY DIFFRACTIONr_mcangle_it2.92324220
X-RAY DIFFRACTIONr_scbond_it4.42332411
X-RAY DIFFRACTIONr_scangle_it5.3624.51799
X-RAY DIFFRACTIONr_rigid_bond_restr2.225310816
X-RAY DIFFRACTIONr_sphericity_free11.653571
X-RAY DIFFRACTIONr_sphericity_bonded5.53537921
LS refinement shellResolution: 1.25→1.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 463 -
Rwork0.271 8936 -
obs--79.94 %

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