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- PDB-1ur2: Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex ... -

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Basic information

Entry
Database: PDB / ID: 1ur2
TitleXylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with arabinofuranose alpha 1,3 linked to xylotriose
ComponentsENDOXYLANASE
KeywordsHYDROLASE / FAMILY 10 / XYLANASE / GLYCOSIDE HYDROLASE / HEMICELLULOSE / XYLAN DEGRADATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases ...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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4beta-beta-xylotriose / Beta-xylanase
Similarity search - Component
Biological speciesCELLVIBRIO MIXTUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPell, G. / Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Mechanisms by which Family 10 Glycoside Hydrolases Bind Decorated Substrates
Authors: Pell, G. / Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Nagy, T. / Clark, S. / Davies, G.J. / Gilbert, H.J.
History
DepositionOct 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENDOXYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0066
Polymers42,9501
Non-polymers1,0565
Water10,647591
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.924, 67.659, 104.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENDOXYLANASE


Mass: 42949.910 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 11-379 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ENGINEERED MUTATION GLU 262 SER IN COORDS / Source: (gene. exp.) CELLVIBRIO MIXTUS (bacteria) / Plasmid: PET 21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TUNER DE3 / References: UniProt: O68541, endo-1,4-beta-xylanase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 414.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylotriose
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a212h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-arabinofuranose-(1-3)-[beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LArafa1-3[DXylpb1-4]DXylpb1-4DXylpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a212h-1a_1-5][a212h-1b_1-5][a211h-1a_1-4]/1-2-3-2/a4-b1_b3-c1_b4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Xylp]{[(4+1)][b-D-Xylp]{[(3+1)][a-L-Araf]{}[(4+1)][b-D-Xylp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 594 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION GLU 271 SER IN THE SWISSPROT DATABASE REFERENCE
Sequence detailsTHE SEQUENCE ON THE DATABASE IS INCORRECT AND WILL BE CHANGED BY THE AUTHORS. THESE DISCREPANCIES ...THE SEQUENCE ON THE DATABASE IS INCORRECT AND WILL BE CHANGED BY THE AUTHORS. THESE DISCREPANCIES ARE F36L, N37I, R38G, R39A, R40A, K216E, T221R, R222G, Y271V, E290D, R291P, M342I. THE SEQUENCE WAS EXPRESSED IN PET21A. THIS ACCOUNTS FOR THE A1M SUBSTITION AND THE ADDITION OF HIS TAG RESIDUES 271-278. THE FIRST 9 RESIDUES IN THE DATABASE HAVE BEEN OMITTED. E262S IS AN ENGINEERED MUTATION.

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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 Å3/Da / Density % sol: 36.6 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 8.5
Details: 0.2M MGCL2 0.1M TRIS HCL PH8.5, 30% PEG 4K, 5% PEG 400., pH 8.50
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mg/mlprotein1drop
210 mMxylooligosaccharide1drop
30.20 M1reservoirMgCl2
40.1 MTris1reservoirpH8.5
530 %PEG40001reservoir
65 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97809
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 15, 2003 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97809 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 42050 / % possible obs: 98.3 % / Redundancy: 3.25 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 1.93
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 2.23 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.93 / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å / Redundancy: 3.25 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 1.6 Å / % possible obs: 90.3 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 1.93

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UQY

1uqy


Resolution: 1.6→19.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.56 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY HAS SOME ATOMS WHICH HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2209 5 %RANDOM
Rwork0.152 ---
obs0.154 42034 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2838 0 68 591 3497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213013
X-RAY DIFFRACTIONr_bond_other_d0.0010.022674
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.9544077
X-RAY DIFFRACTIONr_angle_other_deg1.24436229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81323.878147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84515523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2351519
X-RAY DIFFRACTIONr_chiral_restr0.0830.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02615
X-RAY DIFFRACTIONr_nbd_refined0.2160.2623
X-RAY DIFFRACTIONr_nbd_other0.190.22738
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0950.21687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.272
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.52272
X-RAY DIFFRACTIONr_mcbond_other0.1791713
X-RAY DIFFRACTIONr_mcangle_it1.02622815
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84931484
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.674.51262
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.242 162
Rwork0.212 2905
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.319
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å

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