[English] 日本語
Yorodumi
- PDB-3q5m: Crystal structure of Escherichia coli BamD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q5m
TitleCrystal structure of Escherichia coli BamD
ComponentsUPF0169 lipoprotein yfiO
KeywordsPROTEIN BINDING / Lipoprotein / BamD
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / membrane
Similarity search - Function
Outer membrane protein assembly factor BamD / Outer membrane lipoprotein BamD-like / Outer membrane lipoprotein / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
IODIDE ION / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.604 Å
AuthorsDong, C. / Hou, H. / Yang, X. / Dong, Y. / Shen, Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of Escherichia coli BamD and its functional implications in outer membrane protein assembly
Authors: Dong, C. / Hou, H.F. / Yang, X. / Shen, Y.Q. / Dong, Y.H.
History
DepositionDec 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Database references
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0169 lipoprotein yfiO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5298
Polymers25,6411
Non-polymers8887
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UPF0169 lipoprotein yfiO
hetero molecules

A: UPF0169 lipoprotein yfiO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,05816
Polymers51,2812
Non-polymers1,77714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,-y,-z+3/21
Buried area2460 Å2
ΔGint-2 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.549, 106.549, 65.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

-
Components

#1: Protein UPF0169 lipoprotein yfiO / Outer membrane protein assembly complex subunit YfiO


Mass: 25640.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yfiO / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC02
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.14M KI, 26%-27% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 21, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 11964 / Num. obs: 10307 / % possible obs: 86.2 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 2 / Redundancy: 23.3 % / Rmerge(I) obs: 0.107 / Rsym value: 0.133 / Net I/σ(I): 41.38
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1155 / Rsym value: 0.643 / % possible all: 99.9

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.604→32.602 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 2.49 / σ(I): 2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 1165 10.01 %random
Rwork0.2162 ---
obs0.2207 10307 97.4 %-
all-11964 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.06 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.3238 Å20 Å2-0 Å2
2--3.3238 Å20 Å2
3----6.6477 Å2
Refinement stepCycle: LAST / Resolution: 2.604→32.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 7 21 1722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091731
X-RAY DIFFRACTIONf_angle_d1.1552351
X-RAY DIFFRACTIONf_dihedral_angle_d17.31652
X-RAY DIFFRACTIONf_chiral_restr0.074250
X-RAY DIFFRACTIONf_plane_restr0.006313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6039-2.72230.36021360.32821225X-RAY DIFFRACTION94
2.7223-2.86580.34371360.28131228X-RAY DIFFRACTION94
2.8658-3.04520.33461430.26651277X-RAY DIFFRACTION96
3.0452-3.28010.31941420.24231284X-RAY DIFFRACTION97
3.2801-3.60980.26361470.21931316X-RAY DIFFRACTION99
3.6098-4.13130.20991470.17211333X-RAY DIFFRACTION99
4.1313-5.20160.18521530.16281368X-RAY DIFFRACTION100
5.2016-32.60410.28851610.2351448X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 37.665 Å / Origin y: -0.7724 Å / Origin z: 36.543 Å
111213212223313233
T0.1536 Å2-0.0263 Å2-0.0443 Å2-0.1951 Å20.0291 Å2--0.2221 Å2
L0.4443 °2-0.4265 °2-0.0186 °2-2.5224 °2-1.4925 °2--2.0321 °2
S-0.0235 Å °0.1845 Å °-0.0654 Å °-0.2994 Å °-0.1249 Å °0.2624 Å °0.2468 Å °-0.0469 Å °0.0863 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