[English] 日本語
Yorodumi
- PDB-6qgx: Crystal structure of E.coli BamA beta-barrel in complex with nano... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qgx
TitleCrystal structure of E.coli BamA beta-barrel in complex with nanobody F7
Components
  • NanoF7
  • Outer membrane protein assembly factor BamA
KeywordsMEMBRANE PROTEIN / Beta-Barrel / outer membrane / protein insertion / protein folding / protein maturation
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane
Similarity search - Function
membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin ...membrane protein fhac: a member of the omp85/tpsb transporter family / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / Surface antigen D15-like / POTRA domain / POTRA domain profile. / Bacterial surface antigen (D15) / Omp85 superfamily domain / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane protein assembly factor BamA
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHartmann, J.-B. / Kaur, H. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Seeger, M. / Maier, T. / Hiller, S.
CitationJournal: J.Biomol.Nmr / Year: 2019
Title: Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach.
Authors: Kaur, H. / Hartmann, J.B. / Jakob, R.P. / Zahn, M. / Zimmermann, I. / Maier, T. / Seeger, M.A. / Hiller, S.
History
DepositionJan 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein assembly factor BamA
B: NanoF7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,09413
Polymers59,7232
Non-polymers3,37111
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint45 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.321, 80.335, 135.349
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Outer membrane protein assembly factor BamA


Mass: 46022.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: bamA, yaeT, Z0188, ECs0179 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0A942
#2: Antibody NanoF7


Mass: 13700.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 33% PEG 400, 0.23 M NaCl, 0.05 M sodium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 2.2→49.34 Å / Num. obs: 27754 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.062 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2725 / CC1/2: 0.826 / Rpim(I) all: 0.374 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4n75

4n75


Resolution: 2.2→46.34 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18
RfactorNum. reflection% reflection
Rfree0.2659 1491 5.37 %
Rwork0.2289 --
obs0.2309 27754 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 101 146 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044078
X-RAY DIFFRACTIONf_angle_d0.5875500
X-RAY DIFFRACTIONf_dihedral_angle_d15.2492342
X-RAY DIFFRACTIONf_chiral_restr0.046552
X-RAY DIFFRACTIONf_plane_restr0.003710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2710.35241270.29722369X-RAY DIFFRACTION99
2.271-2.35220.31581460.28212362X-RAY DIFFRACTION99
2.3522-2.44640.31761580.27012335X-RAY DIFFRACTION100
2.4464-2.55770.30051170.26832358X-RAY DIFFRACTION100
2.5577-2.69250.3251270.26892403X-RAY DIFFRACTION99
2.6925-2.86120.30361230.26792366X-RAY DIFFRACTION99
2.8612-3.08210.30791430.25952379X-RAY DIFFRACTION99
3.0821-3.39210.26011360.23762361X-RAY DIFFRACTION99
3.3921-3.88280.27641440.2162393X-RAY DIFFRACTION99
3.8828-4.8910.22511320.17982432X-RAY DIFFRACTION98
4.891-46.35050.24171380.23082505X-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)
14.5564-1.42473.14270.8177-0.983.4087-0.4051-0.6778-0.04721.18590.3088-0.40230.0119-0.05740.03281.07170.1113-0.00570.61490.06590.803215.274-4.009438.8363
20.78521.04361.45131.9041.81253.28720.08430.1058-0.35730.28220.3206-0.40840.38430.5146-0.4080.42150.0719-0.0550.5947-0.05930.655726.04642.958625.2989
34.9682-1.6551-3.06572.62972.64044.8721-0.1749-0.1737-0.2216-0.05960.2923-0.19510.110.5986-0.12830.3413-0.057-0.05610.37650.00680.399218.555719.079532.5406
43.3643-1.4429-0.74823.09112.26793.7304-0.13020.139-0.0349-0.43750.2195-0.3282-0.24940.2267-0.07420.5303-0.10490.02710.46740.04930.52516.668210.032110.8473
59.2181-1.1188-3.15315.07151.2334.3659-0.3132-1.1621-0.32870.8239-0.43991.0316-0.4672-0.38370.61270.4366-0.0243-0.0980.59030.02210.62840.615621.332138.2323
63.94850.239-2.97562.59250.80145.9307-0.0080.03920.1756-0.2514-0.00470.1225-0.1055-0.0621-0.00670.41420.0076-0.10730.3636-0.0340.48516.954516.376221.0029
71.00510.29960.4513.57340.78371.12260.0291-0.16180.28330.33930.13940.81640.082-0.797-0.03660.6685-0.1182-0.12880.824-0.08860.8071-5.6853-12.68290.8984
83.0382-0.25740.31096.44254.13722.65-0.3783-0.59080.5487-0.2548-0.46140.8657-0.0856-0.91820.96360.4629-0.042-0.04650.6606-0.09550.6489-5.2805-4.88373.7075
95.95230.1851-0.68914.50312.30815.251-0.26530.2603-0.2744-0.16470.2097-0.38340.36940.18310.10540.6031-0.04490.01050.5580.03050.36466.8417-4.5761-3.4598
103.31520.37151.08556.2794-4.7758.61820.2397-0.82980.43050.81980.32110.2835-0.9073-1.8891-0.55390.67480.0663-0.02640.884-0.08320.6068-5.26651.77733.0188
112.51060.48932.31584.34882.25733.019-0.0003-0.0783-0.0742-0.1764-0.1048-0.089-0.0849-0.15310.12240.4908-0.050.02980.5194-0.01580.42154.2812-7.6618-0.5573
124.8736-0.1454-2.12046.51640.84339.1902-0.2597-0.115-0.7064-1.0606-0.0642-0.15150.29640.24010.22650.9358-0.0249-0.07840.6508-0.09080.9001-0.9122-14.6532-13.4851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 426 through 453 )
2X-RAY DIFFRACTION2chain 'A' and (resid 454 through 581 )
3X-RAY DIFFRACTION3chain 'A' and (resid 582 through 640 )
4X-RAY DIFFRACTION4chain 'A' and (resid 641 through 709 )
5X-RAY DIFFRACTION5chain 'A' and (resid 710 through 732 )
6X-RAY DIFFRACTION6chain 'A' and (resid 733 through 810 )
7X-RAY DIFFRACTION7chain 'B' and (resid -1 through 14 )
8X-RAY DIFFRACTION8chain 'B' and (resid 15 through 33 )
9X-RAY DIFFRACTION9chain 'B' and (resid 34 through 69 )
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 117 )
12X-RAY DIFFRACTION12chain 'B' and (resid 118 through 124 )

+
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