[English] 日本語
Yorodumi
- PDB-6gki: Structure of E coli MlaC in Variously Loaded States -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6gki
TitleStructure of E coli MlaC in Variously Loaded States
ComponentsProbable phospholipid-binding protein MlaC
KeywordsLIPID TRANSPORT / Lipid Transfer Outer Membranes
Function / homologyTgt2/MlaC superfamily / Toluene tolerance Ttg2/phospholipid-binding protein MlaC / MlaC protein / intermembrane phospholipid transfer / phospholipid transport / outer membrane-bounded periplasmic space / BROMIDE ION / Intermembrane phospholipid transport system binding protein MlaC
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsKnowles, T.J. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P009840/1 United Kingdom
CitationJournal: Nat Microbiol / Year: 2019
Title: Evidence for phospholipid export from the bacterial inner membrane by the Mla ABC transport system.
Authors: Hughes, G.W. / Hall, S.C.L. / Laxton, C.S. / Sridhar, P. / Mahadi, A.H. / Hatton, C. / Piggot, T.J. / Wotherspoon, P.J. / Leney, A.C. / Ward, D.G. / Jamshad, M. / Spana, V. / Cadby, I.T. / ...Authors: Hughes, G.W. / Hall, S.C.L. / Laxton, C.S. / Sridhar, P. / Mahadi, A.H. / Hatton, C. / Piggot, T.J. / Wotherspoon, P.J. / Leney, A.C. / Ward, D.G. / Jamshad, M. / Spana, V. / Cadby, I.T. / Harding, C. / Isom, G.L. / Bryant, J.A. / Parr, R.J. / Yakub, Y. / Jeeves, M. / Huber, D. / Henderson, I.R. / Clifton, L.A. / Lovering, A.L. / Knowles, T.J.
History
DepositionMay 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Probable phospholipid-binding protein MlaC
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,54913
Polymers45,6582
Non-polymers89111
Water1,35175
1
A: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3087
Polymers22,8291
Non-polymers4796
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable phospholipid-binding protein MlaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2416
Polymers22,8291
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.290, 105.290, 96.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-411-

HOH

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

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 24 - 206 / Label seq-ID: 3 - 185

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

-
Components

#1: Protein Probable phospholipid-binding protein MlaC


Mass: 22828.830 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mlaC, yrbC, b3192, JW3159 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0ADV7
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.65 Å3/Da / Density % sol: 66.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: seed grown in (0.1M Na Cacodylate pH 6.5, 2M ammonium sulphate, 0.2M NaCl) seed transferred to drop of (0.09M NaF/Br/I, 0.1M Tris/bicine pH 8.5, 20% glycerol, 10% PEG 4000)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.23→52.64 Å / Num. obs: 30115 / % possible obs: 98.7 % / Redundancy: 18.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.027 / Rrim(I) all: 0.117 / Net I/σ(I): 17.9 / Num. measured all: 559345
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.23-2.2912.12.49219780.490.7222.60389
9.97-52.6416.20.0383980.9990.0090.03999.5

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0216refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UWA

5uwa


Resolution: 2.23→52.64 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 14.017 / SU ML: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.179
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 1573 5.2 %RANDOM
Rwork0.197 ---
obs0.1991 28511 98.66 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso max: 141.72 Å2 / Biso mean: 62.722 Å2 / Biso min: 40.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.63 Å20 Å2
2--1.25 Å2-0 Å2
3----4.06 Å2
Refinement stepCycle: final / Resolution: 2.23→52.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2985 0 16 75 3076
Biso mean--96.08 56.47 -
Num. residues----370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023119
X-RAY DIFFRACTIONr_bond_other_d0.0010.022882
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9614244
X-RAY DIFFRACTIONr_angle_other_deg0.81136713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0795382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22924.737152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60815545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0551520
X-RAY DIFFRACTIONr_chiral_restr0.0910.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213484
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02616
Refine LS restraints NCS

Ens-ID: 1 / Number: 5502 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 82 -
Rwork0.349 1886 -
all-1968 -
obs--88.69 %
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)
12.03250.13831.08620.55820.54893.11330.19080.0148-0.2243-0.0197-0.0237-0.10970.07820.1258-0.16710.02170.0007-0.01510.01380.00460.041664.54327.22434.02
21.15390.2744-0.75041.9440.80715.19350.1549-0.05020.0509-0.06740.0367-0.167-0.16960.2153-0.19160.1855-0.02880.03880.0121-0.01740.084542.6087.85149.031
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 207
2X-RAY DIFFRACTION2B24 - 208

+
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