[English] 日本語
Yorodumi
- PDB-2yh5: Structure of the C-terminal domain of BamC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yh5
TitleStructure of the C-terminal domain of BamC
ComponentsDAPX PROTEIN
KeywordsLIPID BINDING PROTEIN / LIPOPROTEIN / BAM COMPLEX
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell surface / membrane / identical protein binding
Similarity search - Function
Outer membrane protein assembly factor BamC / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / TATA-Binding Protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Outer membrane protein assembly factor BamC / DapX protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 1.25 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 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Feb 5, 2014Group: Refinement description

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DAPX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0883
Polymers13,8981
Non-polymers1902
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.740, 59.120, 31.060
Angle α, β, γ (deg.)90.00, 116.37, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein DAPX PROTEIN / BAMC


Mass: 13898.449 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47548, UniProt: P0A903*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE WAS ASSIGNED DUE TO SUBTILISIN TREATMENT AND X-RAY DATA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.72 Å3/Da / Density % sol: 27.78 % / Description: NONE
Crystal growpH: 6.5 / Details: 25% PEG1000, 0.1 M MES PH 6.5

-
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: 1.28→1.31 Å / Num. obs: 25297 / % possible obs: 98.4 % / Observed criterion σ(I): 2.1 / Redundancy: 5.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.3
Reflection shellResolution: 1.28→1.31 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
SHARPphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 1.25→29.56 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / Stereochemistry target values: MAAIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18387 1332 5 %RANDOM
Rwork0.14643 ---
obs0.14828 25297 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: 13.829 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.13 Å2
2--0.48 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.25→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 10 60 986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.022973
X-RAY DIFFRACTIONr_bond_other_d0.0050.02633
X-RAY DIFFRACTIONr_angle_refined_deg2.1571.9741333
X-RAY DIFFRACTIONr_angle_other_deg1.19731569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.34726.04743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57115164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.244154
X-RAY DIFFRACTIONr_chiral_restr0.1570.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02176
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_it2.8841.5619
X-RAY DIFFRACTIONr_mcbond_other0.9511.5250
X-RAY DIFFRACTIONr_mcangle_it4.32521002
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.293354
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1194.5325
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.58231606
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 98 -
Rwork0.251 1852 -
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)
10.19370.1203-0.03570.3904-0.69571.4455-0.0158-0.02090.1205-0.0866-0.04530.02830.18050.02820.06110.090.00040.01550.0725-0.00950.09425.62225.3463.726
20.99040.0469-0.08780.8036-0.54382.25660.05-0.01140.08390.05330.02680.0625-0.0611-0.1834-0.07680.05060.02880.00890.07650.00870.0562-3.59730.5211.474
30.7136-0.0085-0.43350.5618-0.0231.2965-0.00570.0331-0.05940.0662-0.0304-0.0164-0.0489-0.06020.03610.04380.0073-0.00240.0457-0.00930.07473.54725.76715.6
45.29792.35050.88031.80731.47642.4755-0.08240.1905-0.08590.04740.010.03510.1350.06210.07230.06890.020.00620.0505-0.00810.05116.12920.65713.066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A202 - 227
2X-RAY DIFFRACTION2A228 - 249
3X-RAY DIFFRACTION3A250 - 297
4X-RAY DIFFRACTION4A298 - 320

+
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