[English] 日本語
Yorodumi
- PDB-6xn1: Crystal structure of the GH43_1 enzyme from Xanthomonas citri com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xn1
TitleCrystal structure of the GH43_1 enzyme from Xanthomonas citri complexed with xylose
ComponentsXylosidase
KeywordsHYDROLASE / glycoside hydrolase / GH43 / xylose
Function / homologyGlycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / DI(HYDROXYETHYL)ETHER / beta-D-xylopyranose / Xylosidase
Function and homology information
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMorais, M.A.B. / Tonoli, C.C.C. / Santos, C.R. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2016/19995-0 Brazil
CitationJournal: Nat Commun / Year: 2021
Title: Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations.
Authors: Morais, M.A.B. / Coines, J. / Domingues, M.N. / Pirolla, R.A.S. / Tonoli, C.C.C. / Santos, C.R. / Correa, J.B.L. / Gozzo, F.C. / Rovira, C. / Murakami, M.T.
History
DepositionJul 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Xylosidase
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,65214
Polymers80,4512
Non-polymers1,20112
Water12,106672
1
A: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9188
Polymers40,2261
Non-polymers6937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xylosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7346
Polymers40,2261
Non-polymers5095
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.431, 165.682, 159.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Xylosidase


Mass: 40225.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: xsa, XAC4258 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PET2
#3: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
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

-
Non-polymers , 4 types, 682 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 672 / 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: 2.68 Å3/Da / Density % sol: 54.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M ammonium sulfate, 30% (w/v) Polietilenoglicol 8,000, 0,1 M sodium cacodylate pH 6,5 and 10 % glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.8→48.33 Å / Num. obs: 77797 / % possible obs: 97.1 % / Redundancy: 4.966 % / Biso Wilson estimate: 24.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.062 / Χ2: 0.933 / Net I/σ(I): 16.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.912.8780.5891.873284012818114120.8040.71789
1.91-2.043.5060.2514.444054412039115650.9510.29696.1
2.04-2.214.4040.1587.934809611209109210.9820.1897.4
2.21-2.425.3650.11112.235546210360103380.9940.12399.8
2.42-2.76.3890.0916.9859950939593840.9970.09899.9
2.7-3.126.1780.05825.351258831382970.9980.06399.8
3.12-3.816.1670.03936.7243543708170610.9990.04399.7
3.81-5.386.1990.03543.5934286555855310.9990.03999.5
5.38-36.7396.2230.03545.4419859322131910.9990.03899.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.8refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MLG

4mlg


Resolution: 1.8→36.739 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 3839 4.94 %
Rwork0.1729 73945 -
obs0.1746 77784 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.14 Å2 / Biso mean: 25.98 Å2 / Biso min: 13.34 Å2
Refinement stepCycle: final / Resolution: 1.8→36.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5197 0 76 672 5945
Biso mean--37.34 31.58 -
Num. residues----662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015441
X-RAY DIFFRACTIONf_angle_d1.2447424
X-RAY DIFFRACTIONf_chiral_restr0.054760
X-RAY DIFFRACTIONf_plane_restr0.007973
X-RAY DIFFRACTIONf_dihedral_angle_d13.8151930
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.803-1.82540.45361010.3963242285
1.8254-1.84940.31751450.3047246590
1.8494-1.87470.28951370.2729250990
1.8747-1.90150.32061170.2641254491
1.9015-1.92990.27091310.249260093
1.9299-1.960.27971360.2308262595
1.96-1.99220.25131470.2136269296
1.9922-2.02650.24021330.2033275898
2.0265-2.06340.24351160.2071278999
2.0634-2.10310.23631340.2032274198
2.1031-2.1460.25471280.2085264394
2.146-2.19260.23191460.1948276199
2.1926-2.24360.25031420.1792799100
2.2436-2.29970.21661510.17252800100
2.2997-2.36190.21121350.17222815100
2.3619-2.43140.25941300.1752822100
2.4314-2.50980.22761610.17772778100
2.5098-2.59950.23621410.17562805100
2.5995-2.70360.25191580.17542811100
2.7036-2.82660.2031400.172803100
2.8266-2.97550.20471550.17842836100
2.9755-3.16190.20951450.17222792100
3.1619-3.40580.20951710.17422807100
3.4058-3.74830.19921450.15332847100
3.7483-4.290.16851610.13672845100
4.29-5.40210.13561650.1174286199

+
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