[English] 日本語
Yorodumi
- PDB-8uwv: Crystal structure of BT3984 SusD-like from Bacteroides thetaiotao... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8uwv
TitleCrystal structure of BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)
ComponentsBT3984 SusD-like
KeywordsSUGAR BINDING PROTEIN / SusD-like / High-mannose N-glycan PUL / Bacteroides thetaiotaomicron
Function / homologySusD-like / Susd and RagB outer membrane lipoprotein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / metal ion binding / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsSastre, D.E. / Navarro, M.V.A.S. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM148075-01A1 United States
CitationJournal: To Be Published
Title: Crystal structure of BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)
Authors: Sastre, D.E. / Navarro, M.V.A.S. / Sundberg, E.J.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BT3984 SusD-like
B: BT3984 SusD-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6443
Polymers113,6202
Non-polymers241
Water28,3201572
1
A: BT3984 SusD-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8342
Polymers56,8101
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BT3984 SusD-like


Theoretical massNumber of molelcules
Total (without water)56,8101
Polymers56,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.370, 82.592, 100.265
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BT3984 SusD-like


Mass: 56809.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3984 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A0N7
#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.: 1572 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350 (INDEX G-11)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.08→46.18 Å / Num. obs: 355545 / % possible obs: 91.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 9.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.0476 / Net I/σ(I): 19.05
Reflection shellResolution: 1.08→1.119 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 15911 / CC1/2: 0.943 / Rrim(I) all: 0.254 / % possible all: 41.19

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→46.18 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.139 17777 5 %
Rwork0.1209 --
obs0.1218 355499 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7742 0 1 1572 9315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168013
X-RAY DIFFRACTIONf_angle_d1.77710936
X-RAY DIFFRACTIONf_dihedral_angle_d7.8831098
X-RAY DIFFRACTIONf_chiral_restr0.1071169
X-RAY DIFFRACTIONf_plane_restr0.0131450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.23761120.21652113X-RAY DIFFRACTION17
1.09-1.10.22552700.18545136X-RAY DIFFRACTION42
1.1-1.120.18353770.15477157X-RAY DIFFRACTION58
1.12-1.130.17054430.14048429X-RAY DIFFRACTION69
1.13-1.150.15135040.12779576X-RAY DIFFRACTION78
1.15-1.160.15245680.122110802X-RAY DIFFRACTION88
1.16-1.180.14136300.121111975X-RAY DIFFRACTION97
1.18-1.20.13296320.115711997X-RAY DIFFRACTION98
1.2-1.210.14016390.11512141X-RAY DIFFRACTION99
1.21-1.230.13366450.116612263X-RAY DIFFRACTION100
1.23-1.260.14266460.112212270X-RAY DIFFRACTION100
1.26-1.280.14336470.116312300X-RAY DIFFRACTION100
1.28-1.30.13636470.115612284X-RAY DIFFRACTION100
1.3-1.330.146450.112712261X-RAY DIFFRACTION100
1.33-1.360.13576460.111912265X-RAY DIFFRACTION100
1.36-1.390.14256460.112612280X-RAY DIFFRACTION100
1.39-1.430.13556470.11112296X-RAY DIFFRACTION100
1.43-1.460.13876450.110212251X-RAY DIFFRACTION100
1.46-1.510.13246480.10912306X-RAY DIFFRACTION100
1.51-1.560.12556490.108612343X-RAY DIFFRACTION100
1.56-1.610.13616480.108912305X-RAY DIFFRACTION100
1.61-1.680.12686460.110512270X-RAY DIFFRACTION100
1.68-1.750.13466470.111412304X-RAY DIFFRACTION100
1.75-1.840.13196450.113112259X-RAY DIFFRACTION100
1.84-1.960.12456490.115912328X-RAY DIFFRACTION100
1.96-2.110.12866480.115212300X-RAY DIFFRACTION100
2.11-2.320.12516490.1112342X-RAY DIFFRACTION100
2.32-2.660.13446490.120412332X-RAY DIFFRACTION100
2.66-3.350.14626500.128912355X-RAY DIFFRACTION100
3.35-46.180.15416600.143112528X-RAY DIFFRACTION100

+
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