[English] 日本語
Yorodumi
- PDB-6bt4: Crystal structure of the SLH domain of Sap from Bacillus anthraci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bt4
TitleCrystal structure of the SLH domain of Sap from Bacillus anthracis in complex with a pyruvylated SCWP unit
ComponentsS-layer protein sap
KeywordsSTRUCTURAL PROTEIN / S-layer homology domain / Secondary cell wall polysaccharide / cell wall / anthrax / S-layer
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Chem-KPM / S-layer protein sap
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.306 Å
AuthorsSychantha, D. / Chapman, R.N. / Bamford, N.C. / Boons, G.J. / Howell, P.L. / Clarke, A.J.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)TGC 114045 Canada
Canadian Institutes of Health Research (CIHR)MOP 43998 Canada
CitationJournal: Biochemistry / Year: 2018
Title: Molecular Basis for the Attachment of S-Layer Proteins to the Cell Wall of Bacillus anthracis.
Authors: Sychantha, D. / Chapman, R.N. / Bamford, N.C. / Boons, G.J. / Howell, P.L. / Clarke, A.J.
History
DepositionDec 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: S-layer protein sap
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8694
Polymers22,1821
Non-polymers6873
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.560, 76.560, 97.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

-
Components

#1: Protein S-layer protein sap / Surface array protein / Surface layer protein


Mass: 22182.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#2: Chemical ChemComp-KPM / 2-(acetylamino)-4-O-{2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl}-2-deoxy-beta-D-glucopyranose


Mass: 494.447 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H30N2O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.76 % / Description: bipyrimidal
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate pH 5.5, 2.0 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9996 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9996 Å / Relative weight: 1
ReflectionResolution: 2.3→47.32 Å / Num. obs: 13241 / % possible obs: 99.41 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.05345 / Net I/σ(I): 21.29
Reflection shellResolution: 2.3→2.39 Å / Redundancy: 6 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.95 / Num. unique obs: 1272 / % possible all: 97.92

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
Cootmodel building
PHENIXphasing
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PYW

3pyw


Resolution: 2.306→47.316 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.65
RfactorNum. reflection% reflection
Rfree0.2182 1326 10.02 %
Rwork0.1848 --
obs0.1881 13236 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.306→47.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1261 0 44 31 1336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081330
X-RAY DIFFRACTIONf_angle_d1.0951804
X-RAY DIFFRACTIONf_dihedral_angle_d13.528497
X-RAY DIFFRACTIONf_chiral_restr0.04205
X-RAY DIFFRACTIONf_plane_restr0.004225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3063-2.39860.29171440.23151282X-RAY DIFFRACTION98
2.3986-2.50780.26011420.19511280X-RAY DIFFRACTION100
2.5078-2.640.23031470.19661321X-RAY DIFFRACTION100
2.64-2.80530.24741430.20421299X-RAY DIFFRACTION100
2.8053-3.02190.26371470.23191315X-RAY DIFFRACTION100
3.0219-3.3260.26311450.21641322X-RAY DIFFRACTION100
3.326-3.8070.20271480.16321320X-RAY DIFFRACTION100
3.807-4.79570.18131500.15271352X-RAY DIFFRACTION99
4.7957-47.32580.20461600.18581419X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7375-5.3554.98495.0664-4.86384.72650.0672-0.81741.38010.8491-0.1662-0.7656-0.5630.55460.26610.46170.03090.00950.6025-0.09290.52256.1674-9.5433-5.8486
29.12772.73992.36437.2245-0.83260.98990.4358-1.39730.38430.7197-0.27660.1197-0.04-0.1182-0.15270.490.01020.14370.63790.0110.3942-5.1374-16.2212-8.9443
34.04265.86521.03129.4289-0.4874.46890.9957-1.72161.05760.3556-1.25241.6686-0.4987-0.20270.10710.45230.02780.13550.7003-0.01370.9474-19.7234-9.2742-11.741
45.9028-1.02110.3687.60261.25334.5326-0.03220.27540.253-0.09920.09750.26960.1007-0.3525-0.07420.26470.00210.07060.35540.10310.3976-15.7707-20.562-15.522
56.4199-0.0278-2.76786.1162-0.06427.5032-0.1290.13670.0529-0.28680.13920.5353-0.0199-0.40710.00810.2936-0.0146-0.01150.34440.04260.2987-0.5097-14.0923-27.1873
62.0725-0.75350.3166.31722.36292.4367-0.2760.2275-0.5797-0.3687-0.09480.51030.3984-0.2810.39710.48750.02010.11130.4720.00330.52082.145-22.1421-29.6051
75.5135-1.8163-4.66029.70931.55843.9917-0.1797-0.4218-0.7308-0.5304-0.3663-0.72350.60980.84430.56270.41270.10320.02620.48710.03470.49716.4247-22.2333-20.8339
88.47592.6671-1.16744.0903-5.99619.93-0.0811-0.03020.1679-0.00120.18970.01180.17560.1215-0.14650.35390.03630.10040.35460.00240.35931.4246-9.7638-15.5742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 82 )
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 92 )
4X-RAY DIFFRACTION4chain 'A' and (resid 93 through 130 )
5X-RAY DIFFRACTION5chain 'A' and (resid 131 through 156 )
6X-RAY DIFFRACTION6chain 'A' and (resid 157 through 174 )
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 192 )
8X-RAY DIFFRACTION8chain 'A' and (resid 193 through 209 )

+
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