[English] 日本語
Yorodumi
- PDB-7dnp: Structure of Brucella abortus SagA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dnp
TitleStructure of Brucella abortus SagA
ComponentsSecretion activator protein, hypothetical
KeywordsHYDROLASE / SagA / muramidase / brucella abortus / T4SS
Function / homologyTtsA-like, Glycoside hydrolase family 108 domain / Peptidoglycan binding domain / Glycosyl hydrolase 108 / Predicted Peptidoglycan domain / Lysozyme-like domain superfamily / membrane / Chem-H9U / Secretion activator protein, hypothetical
Function and homology information
Biological speciesBrucella abortus bv. 1 str. 9-941 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHyun, Y. / Ha, N.-C.
CitationJournal: Mol.Cells / Year: 2021
Title: Structure and Function of the Autolysin SagA in the Type IV Secretion System of Brucella abortus .
Authors: Hyun, Y. / Baek, Y. / Lee, C. / Ki, N. / Ahn, J. / Ryu, S. / Ha, N.C.
History
DepositionDec 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 13, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Secretion activator protein, hypothetical
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4772
Polymers19,7811
Non-polymers6971
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8660 Å2
Unit cell
Length a, b, c (Å)79.040, 79.040, 79.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Space group name HallP2ac2ab3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y+1/2,-z,x+1/2
#5: z+1/2,-x+1/2,-y
#6: -y,z+1/2,-x+1/2
#7: -z+1/2,-x,y+1/2
#8: -z,x+1/2,-y+1/2
#9: y+1/2,-z+1/2,-x
#10: x+1/2,-y+1/2,-z
#11: -x,y+1/2,-z+1/2
#12: -x+1/2,-y,z+1/2

-
Components

#1: Protein Secretion activator protein, hypothetical


Mass: 19780.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus bv. 1 str. 9-941 (bacteria)
Strain: 9-941 / Gene: BruAb1_0990 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57DE3
#2: Chemical ChemComp-H9U / (2R)-2-[[(2S)-2-[[(2R)-2-[(2R,3S,4R,5R,6S)-5-acetamido-3-[(2S,3R,4R,5S,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-(hydroxymethyl)-6-oxidanyl-oxan-4-yl]oxypropanoyl]amino]propanoyl]amino]pentanedioic acid


Mass: 696.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44N4O17 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate (pH 4.1), 21% (w/v) polyethylene glycol 4,000, 2 mM Tris(2-chloroethyl) phosphate (TCEP)

-
Data collection

DiffractionMean temperature: 100.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 11424 / % possible obs: 100 % / Redundancy: 30.7 % / Biso Wilson estimate: 23.35 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.009 / Rrim(I) all: 0.056 / Net I/σ(I): 67.5
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 15.6 / Num. unique obs: 570 / CC1/2: 0.989 / CC star: 0.997 / Rpim(I) all: 0.043 / Rrim(I) all: 0.219

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.63 Å / SU ML: 0.1396 / Cross valid method: FREE R-VALUE / σ(F): 1.65 / Phase error: 20.8872
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 598 5.24 %
Rwork0.186 10807 -
obs0.188 11405 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.44 Å2
Refinement stepCycle: LAST / Resolution: 2→45.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 48 70 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311387
X-RAY DIFFRACTIONf_angle_d0.61181875
X-RAY DIFFRACTIONf_chiral_restr0.039215
X-RAY DIFFRACTIONf_plane_restr0.0028236
X-RAY DIFFRACTIONf_dihedral_angle_d14.9644189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20.25061560.18022650X-RAY DIFFRACTION100
2.2-2.520.2441270.19232701X-RAY DIFFRACTION99.93
2.52-3.170.24331530.21252683X-RAY DIFFRACTION100
3.17-45.630.20191620.17162773X-RAY DIFFRACTION99.97

+
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