[English] 日本語
Yorodumi
- PDB-5ay7: A psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ay7
TitleA psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase
Componentsxylanase
KeywordsHYDROLASE / xylanase / GH10 / TIM-barrel fold
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesAegilops speltoides subsp. speltoides (goat grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsZheng, Y. / Li, Y. / Liu, W. / Guo, R.T.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2012AA022209 China
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural insight into potential cold adaptation mechanism through a psychrophilic glycoside hydrolase family 10 endo-beta-1,4-xylanase.
Authors: Zheng, Y. / Li, Y. / Liu, W. / Chen, C.C. / Ko, T.P. / He, M. / Xu, Z. / Liu, M. / Luo, H. / Guo, R.T. / Yao, B. / Ma, Y.
History
DepositionAug 10, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: xylanase
B: xylanase


Theoretical massNumber of molelcules
Total (without water)82,4392
Polymers82,4392
Non-polymers00
Water3,279182
1
A: xylanase


Theoretical massNumber of molelcules
Total (without water)41,2191
Polymers41,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: xylanase


Theoretical massNumber of molelcules
Total (without water)41,2191
Polymers41,2191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.434, 78.346, 89.296
Angle α, β, γ (deg.)90.00, 103.15, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein xylanase /


Mass: 41219.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aegilops speltoides subsp. speltoides (goat grass)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A140UHL2*PLUS, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.5 / Details: 0.1M Tris, pH 8.5, 0.2M Li2SO4, 30% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 42567 / % possible obs: 98.38 % / Redundancy: 3.2 % / Net I/σ(I): 21.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
REFMACdata reduction
HKL-2000data scaling
Cootphasing
RefinementResolution: 2.15→25 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.776 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25738 2069 4.9 %RANDOM
Rwork0.19169 ---
obs0.1948 40478 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.53 Å2
Baniso -1Baniso -2Baniso -3
1-10.59 Å2-0 Å23.7 Å2
2---7.07 Å2-0 Å2
3----4.73 Å2
Refinement stepCycle: 1 / Resolution: 2.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 0 182 5441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195394
X-RAY DIFFRACTIONr_bond_other_d0.0010.024994
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9347306
X-RAY DIFFRACTIONr_angle_other_deg0.868311487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.5465637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04324.846293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.48615920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3871527
X-RAY DIFFRACTIONr_chiral_restr0.0950.2751
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021300
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8555.3652560
X-RAY DIFFRACTIONr_mcbond_other3.8465.3642559
X-RAY DIFFRACTIONr_mcangle_it5.5638.0363193
X-RAY DIFFRACTIONr_mcangle_other5.5628.0383194
X-RAY DIFFRACTIONr_scbond_it4.6025.8582834
X-RAY DIFFRACTIONr_scbond_other4.5985.8542832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9928.5874113
X-RAY DIFFRACTIONr_long_range_B_refined9.05343.9446413
X-RAY DIFFRACTIONr_long_range_B_other8.9743.8786374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.155→2.211 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 152 -
Rwork0.331 2707 -
obs--90.47 %

+
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