[English] 日本語
Yorodumi
- PDB-4hdj: Crystal Structure of BamB from Pseudomonas aeruginosa -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hdj
TitleCrystal Structure of BamB from Pseudomonas aeruginosa
ComponentsOuter membrane protein assembly factor BamB
KeywordsPROTEIN BINDING / beta-propeller / beta-barrel assembly
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function
PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H ...PQQ enzyme repeat / Outer membrane protein assembly factor BamB / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Prokaryotic membrane lipoprotein lipid attachment site profile. / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsJansen, K.B. / Baker, S.L. / Sousa, M.C.
CitationJournal: Plos One / Year: 2012
Title: Crystal structure of BamB from Pseudomonas aeruginosa and functional evaluation of its conserved structural features.
Authors: Jansen, K.B. / Baker, S.L. / Sousa, M.C.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 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: Outer membrane protein assembly factor BamB


Theoretical massNumber of molelcules
Total (without water)38,9431
Polymers38,9431
Non-polymers00
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.984, 82.984, 83.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

21A-513-

HOH

31A-540-

HOH

41A-694-

HOH

51A-764-

HOH

-
Components

#1: Protein Outer membrane protein assembly factor BamB


Mass: 38942.758 Da / Num. of mol.: 1 / Fragment: unp residues 20-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: bamB, PA3800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXJ7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% Tacsimate, 10% PEG , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.15K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→36 Å / Num. all: 28674 / Num. obs: 28674

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 1.85→36 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2053 1463 5.1 %5.1% random selection
Rwork0.1604 ---
all0.1627 28674 --
obs0.1627 28674 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 402 3045
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112687
X-RAY DIFFRACTIONf_angle_d1.5653653
X-RAY DIFFRACTIONf_dihedral_angle_d14.239961
X-RAY DIFFRACTIONf_chiral_restr0.099417
X-RAY DIFFRACTIONf_plane_restr0.008478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8478-1.91390.25791400.18632649X-RAY DIFFRACTION99
1.9139-1.99050.24781490.1832705X-RAY DIFFRACTION100
1.9905-2.08110.23261380.16732708X-RAY DIFFRACTION100
2.0811-2.19080.23621480.16312711X-RAY DIFFRACTION100
2.1908-2.3280.2211590.16792684X-RAY DIFFRACTION100
2.328-2.50770.2141650.16152717X-RAY DIFFRACTION100
2.5077-2.760.21731470.17942720X-RAY DIFFRACTION100
2.76-3.15920.21251400.17252722X-RAY DIFFRACTION99
3.1592-3.97940.20051400.14722775X-RAY DIFFRACTION99
3.9794-36.06840.14981370.14132820X-RAY DIFFRACTION97
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)
10.3883-0.11630.05190.3547-0.14850.0525-0.05510.1138-0.172-0.06590.0648-0.09920.001-0.05690.02520.0619-0.01780.0320.1007-0.04670.126320.79340.467713.9217
20.1742-0.0803-0.05290.06420.04440.0328-0.02760.0515-0.12270.12020.02140.1091-0.04830.03870.00170.1184-0.00170.01560.12190.02110.07926.756141.850526.0627
30.19030.0505-0.07850.18080.07280.08240.0469-0.0870.07450.1023-0.0660.0422-0.04190.0703-0.01580.1503-0.0314-00.1455-0.00330.041215.120754.055231.5705
40.21480.0994-0.18560.1489-0.01160.1960.00650.0177-0.06050.0169-0.0699-0.0382-0.07540.0073-0.010.0839-0.0093-0.00010.0941-0.03320.112733.133955.906118.0465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 28:157 )A28 - 157
2X-RAY DIFFRACTION2( CHAIN A AND RESID 158:192 )A158 - 192
3X-RAY DIFFRACTION3( CHAIN A AND RESID 193:281 )A193 - 281
4X-RAY DIFFRACTION4( CHAIN A AND RESID 282:382 )A282 - 382

+
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