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- PDB-1h4g: Oligosaccharide-binding to family 11 xylanases: both covalent int... -

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Basic information

Entry
Database: PDB / ID: 1h4g
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, 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 speciesBACILLUS AGARADHAERENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.1 Å
AuthorsSabini, E. / Wilson, K.S. / Danielsen, S. / Schulein, M. / Davies, G.J.
CitationJournal: 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: XYLANASE
B: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1687
Polymers46,3112
Non-polymers8575
Water10,917606
1
A: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5363
Polymers23,1561
Non-polymers3802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6324
Polymers23,1561
Non-polymers4763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.061, 75.098, 78.270
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 XYLANASE /


Mass: 23155.547 Da / Num. of mol.: 2 / Fragment: FAMILY 11 XYLANASE CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Details: 2-FLUORO-2-DEOXY-XYLOBIOSIDE COVALENTLY BOUND TO NUCLEOPHILE GLU94 IN THE ACTIVE SITE
Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Production host: BACILLUS LICHENIFORMIS (bacteria) / References: UniProt: Q7SIE3*PLUS, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-2-deoxy-2-fluoro-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 284.236 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a212h-1a_1-5_2*F][a212h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][<C5O2F1>]{[(1+1)][b-D-Xylp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 6
Details: DROP: 2UL PROTEIN (10 MG ML-1 IN 100MM SODIUM ACETATE) PLUS 1UL RESERVOIR RESERVOIR: 100 MM MES PH 6.5, 30% AMMONIUM SULPHATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMsodium acetate1droppH6.0
3100 mMMES1reservoir
430 %ammonium sulfate1reservoirpH6.5
5100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8469
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 1.1→20 Å / Num. obs: 171783 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2 / % possible all: 99
Reflection
*PLUS
Highest resolution: 1.1 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.71

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Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.1→20 Å / SU B: 0.38942 / SU ML: 0.01943 / Cross valid method: THROUGHOUT / ESU R Free: 0.03143
RfactorNum. reflection% reflectionSelection details
Rfree0.181 -5 %RANDOM
Rwork0.158 ---
obs-171783 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 51 606 3920
Refinement
*PLUS
Highest resolution: 1.1 Å / Rfactor obs: 0.158 / Rfactor Rfree: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.039

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