[English] 日本語
Yorodumi
- PDB-2y64: Xylopentaose binding mutated (X-2 L110F) CBM4-2 Carbohydrate Bind... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y64
TitleXylopentaose binding mutated (X-2 L110F) CBM4-2 Carbohydrate Binding Module from a Thermostable Rhodothermus marinus Xylanase
ComponentsXYLANASE
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / endo-1,4-beta-xylanase / xylan catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / metal ion binding
Similarity search - Function
Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...Secretion system C-terminal sorting domain / Carbohydrate-binding, CenC-like / Carbohydrate binding domain / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Xylanase / endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesRHODOTHERMUS MARINUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Authorsvon Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M.
CitationJournal: Glycobiology / Year: 2012
Title: Structural basis for carbohydrate-binding specificity--a comparative assessment of two engineered carbohydrate-binding modules.
Authors: von Schantz, L. / Hakansson, M. / Logan, D.T. / Walse, B. / Osterlin, J. / Nordberg-Karlsson, E. / Ohlin, M.
History
DepositionJan 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source
Item: _audit_author.name / _citation.journal_id_ISSN ..._audit_author.name / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._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_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: XYLANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6984
Polymers17,9401
Non-polymers7593
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.460, 50.680, 62.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein XYLANASE / X-2L110F VARIANT XYLANASE


Mass: 17939.734 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE, RESIDUES 1-165 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): T7 EXPRESS
References: UniProt: Q6V8M0, UniProt: Q7WTN6*PLUS, endo-1,4-beta-xylanase
#2: Polysaccharide beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 678.589 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a212h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, TYR 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, TYR 68 TO PHE ENGINEERED RESIDUE IN CHAIN A, ASP 69 TO ASN ENGINEERED RESIDUE IN CHAIN A, GLU 71 TO GLN ENGINEERED RESIDUE IN CHAIN A, PHE 75 TO LEU ENGINEERED RESIDUE IN CHAIN A, TRP 90 TO ARG ENGINEERED RESIDUE IN CHAIN A, GLN 110 TO ASP ENGINEERED RESIDUE IN CHAIN A, GLU 117 TO HIS
Nonpolymer detailsD-XYLOSE (XYP): XYLOPENTAOSE C5-LINKED XYLOSE.
Sequence detailsTHIS CONSTRUCT STARTS WITH MET (POSITION 1) AS AN INITIATING MET AND ENDS WITH LEU.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M MIB BUFFER PH 6.0, 25 % W/V PEG 1500.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Mar 10, 2010 / Details: MIRRORS
RadiationMonochromator: GERMANIUM CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 30301 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.7 / % possible all: 96.2

-
Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y6H

2y6h


Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1515 0.05 %RANDOM
obs0.143 -92.8 %-
all-28786 --
Solvent computationSolvent model: SWAT
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 48 216 1533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

+
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