[English] 日本語
Yorodumi
- PDB-1v0l: Xylanase Xyn10A from Streptomyces lividans in complex with xylobi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v0l
TitleXylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine at pH 5.8
ComponentsENDO-1,4-BETA-XYLANASE A
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLANASE / XYLAN DEGRADATION / ISOFAGOMINE
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
PIPERIDINE-3,4-DIOL / beta-D-xylopyranose / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesSTREPTOMYCES LIVIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsGloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki, J. / Withers, S.G. / Davies, G.J.
CitationJournal: Chem.Commun.(Camb.) / Year: 2004
Title: Atomic Resolution Analyses of the Binding of Xylobiose-Derived Deoxynojirimycin and Isofagomine to Xylanase Xyn10A
Authors: Gloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki, J. / Withers, S.G. / Davies, G.J.
History
DepositionMar 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...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 / 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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: ENDO-1,4-BETA-XYLANASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3973
Polymers34,1291
Non-polymers2672
Water11,548641
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.018, 46.098, 86.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 42-354
Source method: isolated from a genetically manipulated source
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: Chemical ChemComp-XIF / PIPERIDINE-3,4-DIOL / XYLOSE-DERIVED ISOFAGOMINE


Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONTRIBUTES TO THE HYDROLYSIS OF HEMICELLULOSE, WHICH IS THE MAJOR COMPONENT OF PLANT CELL-WALLS. ...CONTRIBUTES TO THE HYDROLYSIS OF HEMICELLULOSE, WHICH IS THE MAJOR COMPONENT OF PLANT CELL-WALLS. XLNA AND XLNB SEEM TO ACT SEQUENTIALLY ON THE SUBSTRATE TO YIELD XYLOBIOSE AND XYLOSE AS CARBON SOURCES.
Has protein modificationY
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 IS AFTER CLEAVAGE OF THE SIGNAL PEPTIDE. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.3 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL
Crystal growpH: 5.8
Details: 20 MG/ML PROTEIN, 0.1 M MES 18% PEG 5KMME, 7.5% ISOPROPANOL, pH 5.80

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9168
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2003 / Details: TORROIDAL MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 0.98→30 Å / Num. obs: 140638 / % possible obs: 93.4 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 26.7
Reflection shellResolution: 0.98→2.02 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.23 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OD8

1od8


Resolution: 0.98→26.82 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.137 6992 5 %RANDOM
Rwork0.118 ---
obs0.119 133506 93.2 %-
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: 7.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.21 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 0.98→26.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 17 641 2989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212580
X-RAY DIFFRACTIONr_bond_other_d00.022245
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.9063524
X-RAY DIFFRACTIONr_angle_other_deg0.88135246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4165317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.91915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_nbd_refined0.3270.2535
X-RAY DIFFRACTIONr_nbd_other0.2420.22299
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1330.21276
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.350.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.280
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.741.52018
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.10622571
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.62231185
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3654.5951
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: 0.98→1.01 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.169 510
Rwork0.156 9127

+
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