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- PDB-1yna: ENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.0 -

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Basic information

Entry
Database: PDB / ID: 1yna
TitleENDO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.0
ComponentsENDO-1,4-BETA-XYLANASE
KeywordsHYDROLASE / XYLANASE
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
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGruber, K. / Kratky, C.
Citation
Journal: Biochemistry / Year: 1998
Title: Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
Authors: Gruber, K. / Klintschar, G. / Hayn, M. / Schlacher, A. / Steiner, W. / Kratky, C.
#1: Journal: J.Biotechnol. / Year: 1996
Title: Three-Dimensional Structure of Endo-1,4-Beta-Xylanase II from Trichoderma Reesei: Two Conformational States in the Active Site
Authors: Schlacher, A. / Holzmann, K. / Hayn, M. / Steiner, W. / Schwab, H.
#2: Journal: Embo J. / Year: 1994
Title: Three-Dimensional Structure of Endo-1,4-Beta-Xylanase II from Trichoderma Reesei: Two Conformational States in the Active Site
Authors: Torronen, A. / Harkki, A. / Rouvinen, J.
History
DepositionAug 22, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)21,3121
Polymers21,3121
Non-polymers00
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.960, 52.570, 50.470
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE / XYNA


Mass: 21311.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / Strain: TSIKLINSKY / References: UniProt: O43097, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / pH: 4
Details: 5-10% PEG-4000, PH 4.0, T=4 DEG C, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein1drop
22.5-5.0 %(w/v)PEG60001drop
30.1 %(w/v)n-octyl-beta-glycoside1drop
4100 mMcitrate1drop
5PEG60001reservoir
6citrate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Date: Apr 24, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→25.3 Å / Num. obs: 26211 / % possible obs: 83.9 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 7.7
Reflection shellResolution: 1.55→1.59 Å / Rmerge(I) obs: 0.354 / % possible all: 30.7
Reflection shell
*PLUS
% possible obs: 30.7 %

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
SHELXL-93model building
X-PLOR3.1model building
SHELXL-93refinement
X-PLOR3.1refinement
XDSdata reduction
CCP4data scaling
SHELXL-93phasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.3 Å / Num. parameters: 6598 / Num. restraintsaints: 6091 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
obs0.193 -83.9 %
all-26211 -
Solvent computationSolvent model: BABINET'S PRINCIPLE (SWAT)
Displacement parametersBiso mean: 19.6 Å2
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1650
Refinement stepCycle: LAST / Resolution: 1.55→25.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 8 138 1650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d1.4
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.155
Solvent computation
*PLUS
Displacement parameters
*PLUS

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