[English] 日本語
Yorodumi
- PDB-7kmn: Crystal structure of XAC1772, a GH35 xyloglucan-active beta-galac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kmn
TitleCrystal structure of XAC1772, a GH35 xyloglucan-active beta-galactosidase from Xanthomonas citri
ComponentsBeta-galactosidase, GH35 family
KeywordsHYDROLASE / Glycoside Hydrolase Family 35 / Xyloglucan
Function / homology
Function and homology information


beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF5597 / Domain of unknown function (DUF5597) / Glycoside hydrolase, family 42, N-terminal / Beta-galactosidase / Glycoside hydrolase, family 35 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVieira, P.S. / Murakami, M.T.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2016/06509-0 Brazil
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
CitationJournal: Nature Communications / Year: 2021
Title: Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors
Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, ...Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, J.B.L. / Zanphorlin, L.M. / Diogo, J.A. / Lima, E.A. / Grandis, A. / Buckeridge, M.S. / Gozzo, F.C. / Benedetti, C.E. / Polikarpov, I. / Giuseppe, P.O. / Murakami, M.T.
History
DepositionNov 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation ..._pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
Revision 1.2Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Oct 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: Beta-galactosidase, GH35 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0295
Polymers59,6451
Non-polymers3844
Water9,368520
1
A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules

A: Beta-galactosidase, GH35 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,11720
Polymers238,5804
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Unit cell
Length a, b, c (Å)115.820, 115.820, 97.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Beta-galactosidase, GH35 family


Mass: 59644.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria)
Strain: 306 / Gene: XAC1772 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PLM3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 mol/L lithium sulfate 1.26 mol/L ammonium sulfate 0.1 mol/L tris

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2018
RadiationMonochromator: Water-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45873 Å / Relative weight: 1
ReflectionResolution: 1.8→19.863 Å / Num. obs: 59344 / % possible obs: 100 % / Redundancy: 6.582 % / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 9526 / CC1/2: 0.376 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D1I

4d1i


Resolution: 1.8→19.863 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2105 2964 5 %
Rwork0.1769 56324 -
obs0.1786 59288 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 32.2155 Å2 / Biso min: 18.53 Å2
Refinement stepCycle: final / Resolution: 1.8→19.863 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4040 0 20 520 4580
Biso mean--62.94 36.83 -
Num. residues----511
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82930.37321400.353264199
1.8293-1.86080.33671390.31892670100
1.8608-1.89460.3291410.29872675100
1.8946-1.9310.29781400.29542664100
1.931-1.97040.31051410.25942681100
1.9704-2.01320.28561400.24282662100
2.0132-2.060.27791410.2232663100
2.06-2.11140.2521420.20862712100
2.1114-2.16850.24721400.19922646100
2.1685-2.23220.25531400.19552676100
2.2322-2.30410.25541420.21322685100
2.3041-2.38640.22271410.18692685100
2.3864-2.48170.22481400.18432656100
2.4817-2.59450.21991420.17672695100
2.5945-2.73090.22811420.17912697100
2.7309-2.90150.24271410.18412678100
2.9015-3.12480.21811410.19162689100
3.1248-3.43780.19381430.16872707100
3.4378-3.93190.15221410.14372681100
3.9319-4.94110.15851420.12012711100
4.9411-19.8630.17461450.1492750100

+
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://pdbjlvh1.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