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- PDB-1qh7: CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,... -

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Basic information

Entry
Database: PDB / ID: 1qh7
TitleCATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE
ComponentsXYLANASE
KeywordsHYDROLASE / GLYCOSYL HYDROLASE
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
beta-D-xylopyranose / Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesBacillus agaradhaerens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSabini, E. / Sulzenbacher, G. / Dauter, M. / Dauter, Z. / Jorgensen, P.L. / Schulein, M. / Dupont, C. / Davies, G.J. / Wilson, K.S.
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, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)46,6114
Polymers46,3112
Non-polymers3002
Water11,007611
1
A: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3062
Polymers23,1561
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3062
Polymers23,1561
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.860, 75.360, 78.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.95985, -0.280398, -0.008088), (0.279233, 0.957821, -0.067883), (0.026781, 0.062899, 0.997661)
Vector: 33.80553, 43.97223, -0.97119)

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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: B-D-XYLANOPYRANOSIDE PRESENT IN THE ACTIVE SITE / Source: (gene. exp.) Bacillus agaradhaerens (bacteria) / Production host: Bacillus subtilis (bacteria) / References: UniProt: Q7SIE3, endo-1,4-beta-xylanase
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.4 Å3/Da / Density % sol: 48.6 %
Crystal growpH: 6.5 / Details: AMMONIUM SULPHATE 30%, MES 0.1M PH 6.5
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMsodium acetate1drop
3100 mMMES1reservoir
430 %ammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.78→54.2 Å / Num. obs: 40782 / % possible obs: 99.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 14.47 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 5.5 / Net I/σ(I): 27.4
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.7 / Rsym value: 16.2 / % possible all: 98.3
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.176 1285 5 %RANDOM
Rwork0.117 ---
obs-41488 99.1 %-
Displacement parametersBiso mean: 16.49 Å2
Refinement stepCycle: LAST / Resolution: 1.78→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 20 611 3959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1822
X-RAY DIFFRACTIONp_mcangle_it2.8773
X-RAY DIFFRACTIONp_scbond_it2.8222
X-RAY DIFFRACTIONp_scangle_it3.7853
X-RAY DIFFRACTIONp_plane_restr0.0140.02
X-RAY DIFFRACTIONp_chiral_restr0.120.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1070.3
X-RAY DIFFRACTIONp_planar_tor5.57
X-RAY DIFFRACTIONp_staggered_tor13.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.220
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.117
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_chiral_restr / Dev ideal target: 0.15

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