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- PDB-1bk1: ENDO-1,4-BETA-XYLANASE C -

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Basic information

Entry
Database: PDB / ID: 1bk1
TitleENDO-1,4-BETA-XYLANASE C
ComponentsENDO-1,4-B-XYLANASE C
KeywordsHYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region
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 3
Similarity search - Component
Biological speciesAspergillus kawachii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFushinobu, S. / Ito, K. / Konno, M. / Wakagi, T. / Matsuzawa, H.
Citation
Journal: Protein Eng. / Year: 1998
Title: Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH.
Authors: Fushinobu, S. / Ito, K. / Konno, M. / Wakagi, T. / Matsuzawa, H.
#1: Journal: Biosci.Biotechnol.Biochem. / Year: 1992
Title: Purification and Properties of Acid Stable Xylanases from Aspergillus Kawachii
Authors: Ito, K. / Ogasawara, H. / Sugimoto, T. / Ishikawa, T.
#2: Journal: Biosci.Biotechnol.Biochem. / Year: 1992
Title: Cloning and Sequencing of the Xync Gene Encoding Acid Xylanase of Aspergillus Kawachii
Authors: Ito, K. / Iwashita, K. / Iwano, K.
History
DepositionJul 14, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENDO-1,4-B-XYLANASE C


Theoretical massNumber of molelcules
Total (without water)19,8941
Polymers19,8941
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.065, 62.065, 113.291
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ENDO-1,4-B-XYLANASE C / XYLANASE


Mass: 19893.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus kawachii (mold) / Strain: IFO 4308 / Cellular location: EXTRACELLULAR / Gene: XYNC / Plasmid: PUAMXC1 / Cellular location (production host): EXTRACELLULAR / Gene (production host): XYNC / Production host: Aspergillus kawachii (mold) / Strain (production host): IFO 4308 / References: UniProt: P33557, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.2 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 3.5 / Method: vapor diffusion, hanging drop
Details: 0.02ml of protein solution was mixed with 0.01ml of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-8 mg/mlprotein1drop
25 mMacetic acid1drop
3100 mMHEPES-NaOH1reservoir
41.5 Msodium sulphate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 4, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→34.7 Å / Num. obs: 15428 / % possible obs: 98.4 % / Observed criterion σ(I): 0.1 / Redundancy: 8.7 % / Biso Wilson estimate: 27.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.397 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 134544
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRICHODERMA REESEI XYNI, PDB ENTRY 1XYN

1xyn


Resolution: 2→6 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.26 637 4.26 %RANDOM
Rwork0.194 ---
obs0.194 12530 83.9 %-
Displacement parametersBiso mean: 30.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 0 111 1505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.9
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.261 67 3.68 %
Rwork0.309 1031 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor obs: 0.309

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