[English] 日本語
Yorodumi
- PDB-5ldv: Crystal Structures of MOMP from Campylobacter jejuni -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ldv
TitleCrystal Structures of MOMP from Campylobacter jejuni
ComponentsMOMP porin
KeywordsMEMBRANE PROTEIN / Porin
Function / homologyCampylobacter major outer membrane / Campylobacter major outer membrane protein / metal ion binding / N-OCTANE / MOMP porin
Function and homology information
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWallat, G.D. / Ferrara, L.M.G. / Moynie, L. / Naismith, J.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2016
Title: MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded beta-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone.
Authors: Ferrara, L.G. / Wallat, G.D. / Moynie, L. / Dhanasekar, N.N. / Aliouane, S. / Acosta-Gutierrez, S. / Pages, J.M. / Bolla, J.M. / Winterhalter, M. / Ceccarelli, M. / Naismith, J.H.
History
DepositionJun 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MOMP porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8817
Polymers44,1461
Non-polymers7356
Water2,288127
1
A: MOMP porin
hetero molecules

A: MOMP porin
hetero molecules

A: MOMP porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,64421
Polymers132,4393
Non-polymers2,20618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area11670 Å2
ΔGint-61 kcal/mol
Surface area53140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.630, 90.630, 104.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein MOMP porin


Mass: 44146.195 Da / Num. of mol.: 1 / Mutation: T1G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: momp / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q659I5
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.25
Details: 0.05M sodium citrate, 35% (v/v) Peg 400, 0.07 M potassium chloride

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.06733 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06733 Å / Relative weight: 1
ReflectionResolution: 2.1→39.24 Å / Num. obs: 28313 / % possible obs: 99.5 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.89
Reflection shellResolution: 2.1→2.175 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→39.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.949 / SU B: 8.587 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22241 1429 5 %RANDOM
Rwork0.19345 ---
obs0.19497 26883 99.51 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 42.064 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---1.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→39.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3081 0 49 127 3257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023218
X-RAY DIFFRACTIONr_bond_other_d0.0010.022989
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9424351
X-RAY DIFFRACTIONr_angle_other_deg0.69736848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.93325.443158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99615487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.652159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2471
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02785
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_it1.4012.4891625
X-RAY DIFFRACTIONr_mcbond_other1.4012.4891624
X-RAY DIFFRACTIONr_mcangle_it2.133.7162031
X-RAY DIFFRACTIONr_mcangle_other2.133.7162032
X-RAY DIFFRACTIONr_scbond_it1.8562.821593
X-RAY DIFFRACTIONr_scbond_other1.8552.8221594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9434.0962318
X-RAY DIFFRACTIONr_long_range_B_refined5.31320.8613505
X-RAY DIFFRACTIONr_long_range_B_other5.31320.8713506
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 111 -
Rwork0.212 2011 -
obs--99.91 %
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)
11.3752-0.2347-0.33371.0720.22020.77310.0908-0.09970.10320.07340.0148-0.0786-0.0923-0.0177-0.10560.09770.0024-0.02490.102-0.01720.037712.97650.1695.833
22.2833-0.66010.604310.7075-3.86123.11750.0875-0.0796-0.01070.1236-0.08940.084-0.14130.09370.00190.02970.0047-0.00460.1116-0.03620.01498.07644.046.393
32.36070.5824-0.51031.8825-0.45230.74610.09-0.0891-0.2599-0.01350.02810.02370.04060.0267-0.11810.0920.0345-0.03070.0589-0.02610.123120.34532.0851.538
47.4442-1.94242.51946.64964.11694.5666-0.8278-0.42970.43020.95130.31640.39480.29570.0470.51140.4811-0.0788-0.04920.3269-0.04340.174640.31738.65324.462
52.39160.82540.83043.58711.1141.93620.11570.0092-0.1969-0.1266-0.0295-0.25320.15010.0671-0.08620.07230.04960.02610.1358-0.01740.126935.6434.226-1.169
61.63190.44320.78511.67140.07111.05850.00760.064-0.0612-0.10660.0193-0.25450.03750.2268-0.0270.06940.02020.01420.1638-0.0390.121135.9244.743-3.087
73.197-0.8819-2.80981.26381.60566.3082-0.016-0.139-0.0016-0.0890.007-0.2117-0.08320.26250.0090.0705-0.0034-0.01570.0643-0.02440.113230.59755.5381.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 73
2X-RAY DIFFRACTION2A74 - 102
3X-RAY DIFFRACTION3A103 - 223
4X-RAY DIFFRACTION4A224 - 229
5X-RAY DIFFRACTION5A230 - 284
6X-RAY DIFFRACTION6A285 - 365
7X-RAY DIFFRACTION7A366 - 408

+
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