[English] 日本語
Yorodumi
- PDB-2yhc: Structure of BamD from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yhc
TitleStructure of BamD from E. coli
ComponentsUPF0169 LIPOPROTEIN YFIO
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / ESSENTIAL BAM COMPONENT
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
UREA / Outer membrane protein assembly factor BamD
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.8 Å
AuthorsZeth, K. / Albrecht, R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Basis of Outer Membrane Protein Biogenesis in Bacteria.
Authors: Albrecht, R. / Zeth, K.
History
DepositionApr 28, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)26,0202
Polymers25,9601
Non-polymers601
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.112, 33.428, 57.783
Angle α, β, γ (deg.)90.00, 111.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein UPF0169 LIPOPROTEIN YFIO / BAMD


Mass: 25959.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 29-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC02
#2: Chemical ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1.84 Å3/Da / Density % sol: 33.14 % / Description: NONE
Crystal growpH: 7 / Details: 30% PEG 4000, 10% I-PROH, 0.1 M HEPES PH 7.5 .

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 16896 / % possible obs: 99.4 % / Observed criterion σ(I): 3.9 / Redundancy: 6.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.3
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.9 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0071refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 1.8→28.39 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.041 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23262 890 5 %RANDOM
Rwork0.19831 ---
obs0.20007 16896 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20.58 Å2
2---0.44 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 4 84 1792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221774
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0951.9362415
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7945215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21624.0499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.08115289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.731514
X-RAY DIFFRACTIONr_chiral_restr0.1560.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211405
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.321.51063
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31721710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.0053711
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2314.5701
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 65 -
Rwork0.273 1234 -
obs--100 %
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)
14.96560.6217-0.13482.8769-0.36552.79290.04720.20850.44990.0855-0.0983-0.0359-0.36020.20070.05110.2014-0.03990.0180.0290.0270.090628.780731.19166.2709
23.70450.58020.26841.55570.26191.43090.0324-0.0461-0.0120.0721-0.0173-0.1105-0.18930.1161-0.01520.0781-0.02750.00320.0133-0.00190.051330.193923.0110.1827
33.85460.20141.2341.19590.40323.18620.1114-0.1036-0.36960.0263-0.0077-0.11070.15650.031-0.10370.0631-0.00740.00680.00560.01210.084526.760814.279511.5769
47.54013.63340.73613.02230.31043.68880.0437-0.6024-0.5293-0.0239-0.1352-0.21520.1388-0.14120.09150.0665-0.02410.03520.10450.04240.098715.74412.064316.9061
52.90723.6010.85825.2930.9480.6654-0.1410.07760.0458-0.27470.15020.022-0.09480.061-0.00920.0424-0.05340.030.1627-0.02330.09461.6043-0.995214.629
61.7011.40791.63581.8521.43262.49160.0688-0.24540.06640.2088-0.1162-0.0066-0.0401-0.22350.04750.0762-0.03830.02140.2031-0.0130.1274-2.0928-3.456625.8886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 40
2X-RAY DIFFRACTION2A41 - 62
3X-RAY DIFFRACTION3A63 - 84
4X-RAY DIFFRACTION4A85 - 140
5X-RAY DIFFRACTION5A141 - 184
6X-RAY DIFFRACTION6A185 - 233

+
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