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- PDB-1h4h: Oligosaccharide-binding to family 11 xylanases: both covalent int... -

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Basic information

Entry
Database: PDB / ID: 1h4h
TitleOligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre
ComponentsXYLANASE
KeywordsGLYCOSIDE HYDROLASE / XYLANASE / OLIGOSACCHARIDE / TRANSITION-STATE / INTERMEDIATE / MUTANT / BOAT CONFORMATION
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 / 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 ...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 / 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 speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSabini, E. / Wilson, K.S. / Danielsen, S. / Schulein, M. / Davies, G.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
Authors: Sabini, E. / Wilson, K.S. / Danielsen, S. / Schulein, M. / Davies, G.J.
#1: Journal: Chem.Biol. / Year: 1999
Title: Catalysis and Specificity in Enzymatic Glycoside Hydrolysis: A 2,5B Conformation for the Glycosyl-Enzyme Intermediate Revealed by the Structure of the Bacillus Agaradhaerens Family 11 Xylanase.
Authors: Sabini, E. / Sulzenbacher, G. / Dauter, M. / Dauter, Z. / Jorgensen, P.L. / Schulein, M. / Dupont, C. / Davies, G.J. / Wilson, K.S.
History
DepositionMay 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 3.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 3.3Aug 13, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLANASE
B: XYLANASE
C: XYLANASE
D: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9058
Polymers93,2474
Non-polymers1,6574
Water8,809489
1
A: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3121
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3121
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3121
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,3121
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.344, 78.895, 76.273
Angle α, β, γ (deg.)90.00, 91.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
XYLANASE


Mass: 23311.773 Da / Num. of mol.: 4 / Fragment: FAMILY 11 XYLANASE CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: XYLOTRIOSE IN THE ACTIVE SITE / Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: Q7SIE2*PLUS, endo-1,4-beta-xylanase
#2: Polysaccharide
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a212h-1a_1-5][a212h-1b_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION GLU94ALA
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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.5
Details: DROP: 1UL PROTEIN (27 MG ML-1) PLUS 1UL RESERVOIR RESERVOIR: 100 MM MES PH 6.5, 0.8M K2HPO4.3H20/NAH2PO4, 10% MPD
Crystal grow
*PLUS
Temperature: 289 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.8 M1reservoirK2HPO4-3H2O/NaH2PO4
210 %(v/v)MPD1reservoir
3100 mMMES1reservoirpH6.5
427 mg/mlprotein1dropin H2O

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8469
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 53623 / % possible obs: 77.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5 / % possible all: 23.9
Reflection
*PLUS
Highest resolution: 1.9 Å / % possible obs: 77.7 %

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Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QH6

1qh6


Resolution: 1.9→20 Å / SU B: 4.86098 / SU ML: 0.13461 / Cross valid method: THROUGHOUT / ESU R Free: 0.19035
RfactorNum. reflection% reflectionSelection details
Rfree0.241 -5 %RANDOM
Rwork0.184 ---
obs-174031 77.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 112 489 7144
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.043
LS refinement shell
*PLUS
Rfactor Rfree: 0.32 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22

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