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- PDB-1e0x: XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERME... -

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Basic information

Entry
Database: PDB / ID: 1e0x
TitleXYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE AT 1.65 A
ComponentsENDO-1,4-BETA-XYLANASE A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLAN DEGRADATION / GLYCOSYL-ENZYME INTERMEDIATE
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / xylan catabolic process / carbohydrate binding / extracellular region
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Ricin-type beta-trefoil lectin domain / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDucros, V. / Charnock, S.J. / Derewenda, U. / Derewenda, Z.S. / Dauter, Z. / Dupont, C. / Shareck, F. / Morosoli, R. / Kluepfel, D. / Davies, G.J.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Substrate Specificity in Glycoside Hydrolase Family 10. Structural and Kinetic Analysis of the Streptomyces Lividans Xylanase 10A
Authors: Ducros, V. / Charnock, S.J. / Derewenda, U. / Derewenda, Z.S. / Dauter, Z. / Dupont, C. / Shareck, F. / Morosoli, R. / Kluepfel, D. / Davies, G.J.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: Crystal Structure, at 2.6 A Resolution, of the Streptomyces Lividans Xylanase A, a Member of the F Family of B-1,4-D-Glycanases
Authors: Derewenda, U. / Swenson, L. / Green, R. / Wei, Y. / Morosoli, R. / Shareck, F. / Kluepfel, D. / Derewenda, Z.S.
History
DepositionApr 10, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2001Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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 / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 1, 2024Group: 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

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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 A
B: ENDO-1,4-BETA-XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1047
Polymers68,2592
Non-polymers8455
Water12,917717
1
A: ENDO-1,4-BETA-XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5984
Polymers34,1291
Non-polymers4683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENDO-1,4-BETA-XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5063
Polymers34,1291
Non-polymers3762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.210, 81.060, 72.810
Angle α, β, γ (deg.)90.00, 102.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99908, -0.04144, 0.0114), (0.04211, 0.9969, -0.06652), (-0.00861, 0.06694, 0.99772)
Vector: 15.98502, 2.67231, 35.57695)

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Components

#1: Protein ENDO-1,4-BETA-XYLANASE A / XYLANASE A / 1 / 4-BETA-D-XYLAN XYLANOHYDROLASE A


Mass: 34129.457 Da / Num. of mol.: 2 / Fragment: CATALYTIC MODULE, RESIDUES 32-450
Source method: isolated from a genetically manipulated source
Details: GLYCOSYL ENXYME INTERMEDIATE. COVALENT LINK BETWEEN GLU 236 AND THE SUBSTRATE
Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): IAF 19 / References: UniProt: P26514, 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE ...THE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE PDB FILE IF AFTER CLEAVAGE OF THE SIGNAL PEPTIDE. THE LAST 4 RESIDUES ARE INVISIBLE IN DENSITY.

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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: 2.7 Å3/Da / Density % sol: 44 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLISED WITH 18 % PEG 5000 AS PRECIPITANT, 100MM HEPES PH 7.5 AS BUFFER, 10% ISOPROPANOL, CRYSTAL WERE SOAKED IN PRESENCE OF POWDERED SUBSTRATE FOR 12 HOURS. 15% GLYCEROL ...Details: PROTEIN WAS CRYSTALLISED WITH 18 % PEG 5000 AS PRECIPITANT, 100MM HEPES PH 7.5 AS BUFFER, 10% ISOPROPANOL, CRYSTAL WERE SOAKED IN PRESENCE OF POWDERED SUBSTRATE FOR 12 HOURS. 15% GLYCEROL WAS ADDED AS CRYOPROTECTANT
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 Msodium HEPES1reservoir
218 %(w/v)PEG50001reservoir
330 mg/mlprotein1drop
410 %(v/v)isopropanol1drop

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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: Nov 15, 1997 / Details: LONG MIRRORS (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. obs: 66881 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 35.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 12.9 / % possible all: 94
Reflection
*PLUS
Lowest resolution: 15 Å / % possible obs: 99 %
Reflection shell
*PLUS
% possible obs: 94 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE AT 1.2

Resolution: 1.65→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DOUBLY CONFIGURATED DISULPHIDE BOND BETWEEN CYS168 AND CYS201
RfactorNum. reflection% reflectionSelection details
Rfree0.162 3381 5 %RANDOM
Rwork0.126 ---
obs-63415 99 %-
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 54 717 5531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.4483
X-RAY DIFFRACTIONp_mcangle_it1.9945
X-RAY DIFFRACTIONp_scbond_it2.3014
X-RAY DIFFRACTIONp_scangle_it2.8856
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.1210.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.140.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor12.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.12
Solvent computation
*PLUS
Displacement parameters
*PLUS

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