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- PDB-1ref: ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE -

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Basic information

Entry
Database: PDB / ID: 1ref
TitleENDO-1,4-BETA-XYLANASE II COMPLEX WITH 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE
ComponentsENDO-1,4-BETA-XYLANASE II
KeywordsHYDROLASE / XYLANASE / XYLAN DEGRADATION
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
BENZOIC ACID / (2R)-oxiran-2-ylmethyl beta-D-xylopyranoside / Endo-1,4-beta-xylanase 2
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsRouvinen, J. / Havukainen, R. / Torronen, A.
Citation
Journal: Biochemistry / Year: 1996
Title: Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei.
Authors: Havukainen, R. / Torronen, A. / Laitinen, T. / Rouvinen, J.
#1: 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
DepositionDec 21, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _chem_comp.pdbx_synonyms / _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 II
B: ENDO-1,4-BETA-XYLANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0054
Polymers41,6772
Non-polymers3282
Water4,504250
1
A: ENDO-1,4-BETA-XYLANASE II


Theoretical massNumber of molelcules
Total (without water)20,8381
Polymers20,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENDO-1,4-BETA-XYLANASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1673
Polymers20,8381
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.340, 60.880, 37.890
Angle α, β, γ (deg.)90.00, 94.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9874, -0.007, 0.158), (-0.0066, -1, -0.003), (0.158, 0.0019, -0.9874)
Vector: 40.0213, 57.4837, 12.6331)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE II / XYNII


Mass: 20838.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / Strain: TRICHODERMA REESEI RUT-C30 / References: UniProt: P36217, endo-1,4-beta-xylanase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Sugar ChemComp-C3X / (2R)-oxiran-2-ylmethyl beta-D-xylopyranoside / 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE / (2R)-oxiran-2-ylmethyl beta-D-xyloside / (2R)-oxiran-2-ylmethyl D-xyloside / (2R)-oxiran-2-ylmethyl xyloside


Type: D-saccharide / Mass: 206.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45 %
Crystal grow
*PLUS
pH: 4.2 / Method: vapor diffusion, hanging drop / Details: Torronen, A., (1993) J. Mol. Biol., 233, 313.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMsodium acetate1drop
325 %ammonium sulfate1drop
425 %ammonium sulfate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 2, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 30167 / % possible obs: 85.5 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. measured all: 82450 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 60.3 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 1.8→8 Å / σ(F): 1
RfactorNum. reflection
Rfree0.229 -
Rwork0.181 -
obs0.181 26750
Displacement parametersBiso mean: 22.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 25 250 3235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_deg27.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9

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