[English] 日本語
Yorodumi
- PDB-9bam: Surface glycan-binding protein A (SGBP-A, SusD-like) from a mixed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bam
TitleSurface glycan-binding protein A (SGBP-A, SusD-like) from a mixed-linkage beta-glucan utilization locus in Segatella copri
ComponentsSurface glycan-binding protein A (SGBP-A)
KeywordsSUGAR BINDING PROTEIN / glycan-binding protein / SGBP-A / mixed-linkage beta-glucan / Segatella copri
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesSegatella copri DSM 18205 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCordeiro, R.L. / Golisch, B. / Brumer, H. / Van Petegem, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The molecular basis of cereal mixed-linkage beta-glucan utilization by the human gut bacterium Segatella copri.
Authors: Golisch, B. / Cordeiro, R.L. / Fraser, A.S.C. / Briggs, J. / Stewart, W.A. / Van Petegem, F. / Brumer, H.
History
DepositionApr 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface glycan-binding protein A (SGBP-A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1982
Polymers67,1741
Non-polymers241
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.877, 76.849, 99.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Surface glycan-binding protein A (SGBP-A)


Mass: 67174.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segatella copri DSM 18205 (bacteria) / Gene: PREVCOP_05098 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: D1PD12
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl (pH 8.5) and 26% (w/v) Polyethylene glycol (PEG) 8,000
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→33.56 Å / Num. obs: 33784 / % possible obs: 99.31 % / Redundancy: 2 % / Biso Wilson estimate: 27.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0449 / Net I/σ(I): 8.41
Reflection shellResolution: 2.05→2.123 Å / Rmerge(I) obs: 0.2893 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 3338 / CC1/2: 0.958

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→33.56 Å / SU ML: 0.2884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7793
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 2558 4.02 %
Rwork0.1853 61046 -
obs0.1872 33784 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.15 Å2
Refinement stepCycle: LAST / Resolution: 2.05→33.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 1 204 4501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074430
X-RAY DIFFRACTIONf_angle_d0.84776024
X-RAY DIFFRACTIONf_chiral_restr0.0464621
X-RAY DIFFRACTIONf_plane_restr0.0081800
X-RAY DIFFRACTIONf_dihedral_angle_d5.7767603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.35871420.27573402X-RAY DIFFRACTION99.16
2.09-2.130.3231410.25813383X-RAY DIFFRACTION98.08
2.13-2.180.28891370.25083365X-RAY DIFFRACTION98.4
2.18-2.230.29361470.2343412X-RAY DIFFRACTION99.72
2.23-2.280.3161390.22973407X-RAY DIFFRACTION99.41
2.28-2.350.26361450.21873395X-RAY DIFFRACTION99.35
2.35-2.420.29021420.2113405X-RAY DIFFRACTION99.75
2.42-2.490.3141400.20593401X-RAY DIFFRACTION99.24
2.49-2.580.29261440.20143449X-RAY DIFFRACTION98.93
2.58-2.690.22381420.20283338X-RAY DIFFRACTION98.61
2.69-2.810.24351410.19263403X-RAY DIFFRACTION99.38
2.81-2.960.22191450.19143432X-RAY DIFFRACTION99.31
2.96-3.140.24591400.18223400X-RAY DIFFRACTION99.38
3.14-3.380.19441420.17183360X-RAY DIFFRACTION98.76
3.38-3.720.22131440.15893399X-RAY DIFFRACTION99.08
3.72-4.260.15151420.13993408X-RAY DIFFRACTION99.05
4.26-5.360.18981410.16353314X-RAY DIFFRACTION97.21
5.37-33.560.24171440.17133373X-RAY DIFFRACTION98.08
Refinement TLS params.Method: refined / Origin x: -16.9458993826 Å / Origin y: 16.4927621231 Å / Origin z: -22.3935806108 Å
111213212223313233
T0.217091160053 Å2-0.0190927184757 Å20.00599849988049 Å2-0.227193665136 Å20.00152173577047 Å2--0.217143385241 Å2
L0.566337972539 °20.0771795625767 °20.0531792612275 °2-0.581590121284 °20.139225439669 °2--0.394519670163 °2
S0.0214588777923 Å °-0.0583458562917 Å °-0.0121006858235 Å °-0.0141538655011 Å °-0.00517567272737 Å °-0.0862021535676 Å °-0.0364696017078 Å °0.0883234248397 Å °2.15376308917E-5 Å °
Refinement TLS groupSelection details: all

+
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