[English] 日本語
Yorodumi
- PDB-2yh9: Crystal structure of the dimeric BamE from E. coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yh9
TitleCrystal structure of the dimeric BamE from E. coli
ComponentsSMALL PROTEIN A
KeywordsMEMBRANE PROTEIN / LIPOPROTEIN / 3D DOMAIN SWAP
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / protein-macromolecule adaptor activity / response to antibiotic / identical protein binding / membrane
Similarity search - Function
Beta-lactamase Inhibitory Protein; Chain:B, domain 1 / Beta-lactamase Inhibitory Protein; Chain:B, domain 1 - #10 / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane protein assembly factor BamE domain / BamE-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamE
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references / Version format compliance
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
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_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SMALL PROTEIN A
B: SMALL PROTEIN A
C: SMALL PROTEIN A


Theoretical massNumber of molelcules
Total (without water)29,7233
Polymers29,7233
Non-polymers00
Water3,135174
1
A: SMALL PROTEIN A
B: SMALL PROTEIN A
C: SMALL PROTEIN A

A: SMALL PROTEIN A
B: SMALL PROTEIN A
C: SMALL PROTEIN A


Theoretical massNumber of molelcules
Total (without water)59,4466
Polymers59,4466
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19110 Å2
ΔGint-116.1 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.660, 96.520, 50.490
Angle α, β, γ (deg.)90.00, 134.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2024-

HOH

21C-2019-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 3 / Auth seq-ID: 10 - 60 / Label seq-ID: 15 - 65

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

-
Components

#1: Protein SMALL PROTEIN A / BAME PROTEIN


Mass: 9907.614 Da / Num. of mol.: 3 / Fragment: RESIDUES 34-113
Source method: isolated from a genetically manipulated source
Details: LIPOPROTEIN SMPA/BAME / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A937
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.62 % / Description: NONE
Crystal growpH: 7.5 / 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: 0.979
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 21093 / % possible obs: 100 % / Observed criterion σ(I): 2.8 / Redundancy: 5.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.7
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.8→22.29 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.828 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22859 1111 5 %RANDOM
Rwork0.18121 ---
obs0.18366 21093 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: 21.797 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20.69 Å2
2---0.61 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1563 0 0 174 1737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221613
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9332201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53924.79573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.86157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2253
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211231
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_it1.5481.51002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5421637
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7093611
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.5014.5562
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.50231613
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A203tight positional0.110.05
2B203tight positional0.180.05
3C203tight positional0.120.05
1A193loose positional0.135
2B193loose positional0.215
3C193loose positional0.145
1A203tight thermal0.310.5
2B203tight thermal0.290.5
3C203tight thermal0.320.5
1A193loose thermal0.3110
2B193loose thermal0.3410
3C193loose thermal0.2910
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 82 -
Rwork0.263 1549 -
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)
12.0115-1.2436-1.67741.15890.59831.896-0.08940.3585-0.17110.0323-0.11560.04490.1056-0.41790.2050.0189-0.0363-0.00890.1653-0.03080.0564-18.45342.843.846
20.80830.4706-0.95050.6069-0.68751.6628-0.0971-0.08-0.1559-0.0862-0.0715-0.08050.23230.1390.16860.06360.03150.00470.07130.03890.0773.09434.4948.438
33.30361.7525-6.902311.3828-8.486216.6572-0.2011-0.0746-0.0021-0.4810.0454-0.37360.61060.12420.15570.1460.05450.07140.0260.02020.18865.57126.5926.694
41.28851.0784-4.30096.35912.468421.5786-0.45750.5235-0.0592-1.77190.7043-0.4630.149-1.4969-0.24680.5581-0.26640.11740.2286-0.03850.067-7.01463.104-18.952
50.24560.0414-0.09830.4367-0.5691.49730.0147-0.00960.0420.0609-0.01750.0408-0.1218-0.03050.00290.04860.0069-0.02880.0425-0.0010.053-1.80157.8295.486
60.2308-0.2999-0.416822.7676-1.86751.0636-0.0427-0.0844-0.09930.9078-0.12810.1735-0.07940.11320.17080.16190.04020.03750.18450.0130.0559-3.68457.23319.443
732.70150-7.04829.7256026.95080.93880.15950.43490.5899-0.1237-0.7403-0.68870.4029-0.81520.09170.0148-0.01410.06750.04610.20557.7530.00518.032
81.6761-2.09130.31543.0099-0.54530.1187-0.08970.0347-0.16550.0520.0383-0.00380.0102-0.02310.05130.0668-0.02310.03460.0832-0.01330.1452-1.82937.27714.462
91.00540.9284-1.36571.1162-1.06562.0798-0.00070.1060.03360.0527-0.01020.058-0.0096-0.24580.01090.04910.0104-0.0160.12150.01680.0703-15.19451.1544.904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 28
2X-RAY DIFFRACTION2A29 - 64
3X-RAY DIFFRACTION3A65 - 70
4X-RAY DIFFRACTION4B4 - 11
5X-RAY DIFFRACTION5B12 - 64
6X-RAY DIFFRACTION6B65 - 72
7X-RAY DIFFRACTION7C5 - 11
8X-RAY DIFFRACTION8C12 - 32
9X-RAY DIFFRACTION9C33 - 71

+
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