[English] 日本語
Yorodumi
- PDB-8y1m: Xylanase R from Bacillus sp. TAR-1 complexed with xylobiose. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8y1m
TitleXylanase R from Bacillus sp. TAR-1 complexed with xylobiose.
ComponentsEndo-1,4-beta-xylanase A
KeywordsHYDROLASE / GH10 / Thermostability / Xylanase / Xylobiose
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / 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 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
4beta-beta-xylobiose / ACETATE ION / DI(HYDROXYETHYL)ETHER / Endo-1,4-beta-xylanase A
Similarity search - Component
Biological speciesBacillus sp. TAR1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamura, T. / Kuwata, K. / Takita, T. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)30397559 Japan
CitationJournal: Sci Rep / Year: 2024
Title: Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
Authors: Nakamura, T. / Takita, T. / Kuwata, K. / Mizutani, K. / Mikami, B. / Nakamura, S. / Yasukawa, K.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Endo-1,4-beta-xylanase A
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,19431
Polymers84,0622
Non-polymers3,13229
Water9,872548
1
A: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,85518
Polymers42,0311
Non-polymers1,82417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-11 kcal/mol
Surface area15000 Å2
MethodPISA
2
B: Endo-1,4-beta-xylanase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,33913
Polymers42,0311
Non-polymers1,30812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.702, 53.335, 96.567
Angle α, β, γ (deg.)90.000, 93.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Endo-1,4-beta-xylanase A / Xylanase A / 1 / 4-beta-D-xylan xylanohydrolase A


Mass: 42031.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. TAR1 (bacteria) / Gene: xynA, BH2120 / Plasmid: pET-21B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07528, endo-1,4-beta-xylanase
#2: Polysaccharide
beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 282.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-xylobiose
DescriptorTypeProgram
DXylpb1-4DXylpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a212h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{}}LINUCSPDB-CARE

-
Non-polymers , 6 types, 573 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.08 % / Description: lectangle plate
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: 0.02 M CaCl2, 0.1 M CH3COONa, 22% v/v 2-methyl-2,4-pentanediol, 0.35 M xylobiose

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 82976 / % possible obs: 97.5 % / Redundancy: 3.39 % / Biso Wilson estimate: 24.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.054 / Net I/σ(I): 16.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 12885 / CC1/2: 0.846 / Rrim(I) all: 0.565 / % possible all: 94.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.26 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2021 4143 5 %
Rwork0.166 78701 -
obs0.1677 82844 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5914 0 195 548 6657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00696447
X-RAY DIFFRACTIONf_angle_d0.86458792
X-RAY DIFFRACTIONf_chiral_restr0.0539906
X-RAY DIFFRACTIONf_plane_restr0.0051150
X-RAY DIFFRACTIONf_dihedral_angle_d15.86962411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.37691300.32792487X-RAY DIFFRACTION92.9
1.82-1.840.27621330.26152525X-RAY DIFFRACTION94.36
1.84-1.860.27241350.2522548X-RAY DIFFRACTION97.39
1.86-1.880.28011360.23312589X-RAY DIFFRACTION96.98
1.88-1.910.43761360.32622580X-RAY DIFFRACTION95.5
1.91-1.930.43791330.36962533X-RAY DIFFRACTION97.09
1.93-1.960.23761390.20972636X-RAY DIFFRACTION98.65
1.96-1.990.22851380.19482621X-RAY DIFFRACTION98.19
1.99-2.020.22211390.18692649X-RAY DIFFRACTION99.57
2.02-2.050.22331390.18612639X-RAY DIFFRACTION97.85
2.05-2.090.24551370.19412596X-RAY DIFFRACTION99.27
2.09-2.130.23251400.17532671X-RAY DIFFRACTION98.63
2.13-2.170.18791370.17122599X-RAY DIFFRACTION99.17
2.17-2.210.22341410.17982678X-RAY DIFFRACTION99.16
2.21-2.260.35061320.2722503X-RAY DIFFRACTION94.51
2.26-2.310.20481380.19362617X-RAY DIFFRACTION97.21
2.31-2.370.1961370.16772613X-RAY DIFFRACTION99.35
2.37-2.440.19241410.15222676X-RAY DIFFRACTION98.84
2.44-2.510.17051400.15782648X-RAY DIFFRACTION99.46
2.51-2.590.19761400.15922658X-RAY DIFFRACTION98.87
2.59-2.680.20181400.16382659X-RAY DIFFRACTION99.08
2.68-2.790.21571400.16162658X-RAY DIFFRACTION99.57
2.79-2.920.20031400.15792661X-RAY DIFFRACTION98.98
2.92-3.070.22721400.16342664X-RAY DIFFRACTION98.73
3.07-3.260.17711380.15032625X-RAY DIFFRACTION98.54
3.26-3.510.17911390.14092652X-RAY DIFFRACTION97.59
3.51-3.870.16351400.12292650X-RAY DIFFRACTION97.93
3.87-4.430.141410.11672678X-RAY DIFFRACTION98.7
4.43-5.570.16571410.13322690X-RAY DIFFRACTION98.71
5.57-44.260.18141430.17332698X-RAY DIFFRACTION95.59

+
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