[English] 日本語
Yorodumi
- PDB-1uqy: Xylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uqy
TitleXylanase Xyn10B mutant (E262S) from Cellvibrio mixtus in complex with xylopentaose
ComponentsENDOXYLANASE
KeywordsHYDROLASE / FAMILY 10 / XYLANASE / GLYCOSIDE HYDROLASE / HEMICELLULOSE / XYLAN DEGRADATION
Function / homology
Function and homology information


endo-1,4-beta-xylanase / endo-1,4-beta-xylanase activity / 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
Biological speciesCELLVIBRIO MIXTUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 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 23, 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 / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDOXYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9354
Polymers42,9501
Non-polymers9853
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.158, 67.901, 104.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Type: oligosaccharide / Mass: 414.360 Da / Num. of mol.: 1
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: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 546.474 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a212h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLU 271 SER AS BASED ON THE SWISSPROT DATABASE NUMBERING.
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 36.6 %
Crystal growpH: 8 / Details: 0.2M MGCL2 0.1M TRIS HCL PH8, 30% PEG 4K, pH 8.00
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.20 M1reservoirMgCl2
20.1 MTris1reservoirpH8.0
330 %PEG40001reservoir
425 mg/mlprotein1drop
510 mMxylooligosaccharide1drop

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2003 / Details: OSMICS
RadiationMonochromator: MULTI-LAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. obs: 34539 / % possible obs: 99.6 % / Redundancy: 6.02 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 46
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 5.49 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 10.35 / % possible all: 98.7
Reflection
*PLUS
Highest resolution: 1.72 Å / Lowest resolution: 20 Å / Redundancy: 6.02 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 10.35

-
Processing

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

1clx


Resolution: 1.72→56.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.774 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.103 / 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
Rfree0.186 1816 5 %RANDOM
Rwork0.14 ---
obs0.142 34539 99.5 %-
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: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.72→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 66 562 3429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212960
X-RAY DIFFRACTIONr_bond_other_d0.0010.022633
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.964010
X-RAY DIFFRACTIONr_angle_other_deg0.86536125
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2945344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57324.014142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01115511
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2281518
X-RAY DIFFRACTIONr_chiral_restr0.1020.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
X-RAY DIFFRACTIONr_nbd_refined0.2230.2619
X-RAY DIFFRACTIONr_nbd_other0.1910.22708
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1571.52232
X-RAY DIFFRACTIONr_mcbond_other0.2471705
X-RAY DIFFRACTIONr_mcangle_it1.34722780
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.531453
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6174.51230
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: 1.72→1.76 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.253 125
Rwork0.178 2485
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.539
LS refinement shell
*PLUS
Lowest resolution: 1.78 Å

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more