[English] 日本語
Yorodumi
- PDB-4hvz: Crystal structure of brucella abortus immunogenic BP26 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hvz
TitleCrystal structure of brucella abortus immunogenic BP26 protein
Components26 kDa periplasmic immunogenic protein
KeywordsMEMBRANE PROTEIN / multimerization / SIMPL domain / infection
Function / homology
Function and homology information


periplasmic space / DNA damage response
Similarity search - Function
Protein of unknown function (DUF541), domain 1 / Protein of unknown function (DUF541), domain 2 / Interleukin-1 receptor-associated kinase 1-binding protein 1/DUF541 / : / Protein of unknown function (DUF541) / Translation Initiation Factor IF3 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
26 kDa periplasmic immunogenic protein
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.5 Å
AuthorsKim, D. / Park, J. / Oh, B. / Song, J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Brucella Immunogenic BP26 Forms a Channel-like Structure.
Authors: Kim, D. / Park, J. / Kim, S.J. / Soh, Y.M. / Kim, H.M. / Oh, B.H. / Song, J.J.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein


Theoretical massNumber of molelcules
Total (without water)95,2084
Polymers95,2084
Non-polymers00
Water00
1
A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein

A: 26 kDa periplasmic immunogenic protein
B: 26 kDa periplasmic immunogenic protein
C: 26 kDa periplasmic immunogenic protein
D: 26 kDa periplasmic immunogenic protein


Theoretical massNumber of molelcules
Total (without water)380,83416
Polymers380,83416
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-11
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_554y,x,-z-11
Buried area83660 Å2
ΔGint-438 kcal/mol
Surface area141830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.086, 203.086, 207.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein
26 kDa periplasmic immunogenic protein


Mass: 23802.096 Da / Num. of mol.: 4 / Fragment: BP26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: S19 / Gene: bp26, BAbS19_I13950 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q44642

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.61 Å3/Da / Density % sol: 78.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.4M AMS, 100mM NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 26996 / Observed criterion σ(F): 0 / Redundancy: 5.9 % / Rsym value: 0.08 / Net I/σ(I): 31.9
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 3.8 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.5→29.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 101166.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2448 10 %RANDOM 10%
Rwork0.237 ---
obs-24457 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.6865 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 121.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0 Å2-0 Å2
2---0.94 Å2-0 Å2
3---1.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 3.5→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6340 0 0 0 6340
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.721.5
X-RAY DIFFRACTIONc_mcangle_it7.262
X-RAY DIFFRACTIONc_scbond_it7.112
X-RAY DIFFRACTIONc_scangle_it9.582.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 360 10 %
Rwork0.331 3249 -
obs--79.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

+
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