[English] 日本語
Yorodumi
- PDB-4aeq: Crystal structure of the dimeric immunity protein Cmi solved by d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aeq
TitleCrystal structure of the dimeric immunity protein Cmi solved by direct methods (Arcimboldo)
ComponentsCOLICIN-M IMMUNITY PROTEIN
KeywordsIMMUNE SYSTEM / 3D DOMAIN SWAP
Function / homologyYebF/Cmi domain profile. / YebF/Colicin-M immunity protein / YebF/Cmi superfamily / YebF-like protein / bacteriocin immunity / PHOSPHATE ION / Colicin-M immunity protein
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.892 Å
AuthorsZeth, K. / Patzer, S.I. / Albrecht, R. / Uson, I. / Braun, V.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: The Crystal Structure of the Dimeric Colicin M Immunity
Authors: Uson, I. / Patzer, S.I. / Dayana Rodriguez, D.D. / Braun, V. / Zeth, K.
History
DepositionJan 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Other
Revision 1.2Apr 18, 2012Group: Other
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: COLICIN-M IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7652
Polymers11,6701
Non-polymers951
Water97354
1
A: COLICIN-M IMMUNITY PROTEIN
hetero molecules

A: COLICIN-M IMMUNITY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5304
Polymers23,3402
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5650 Å2
ΔGint-58.8 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.058, 83.552, 38.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

-
Components

#1: Protein COLICIN-M IMMUNITY PROTEIN / CMI / MICROCIN-M IMMUNITY PROTEIN


Mass: 11670.021 Da / Num. of mol.: 1 / Fragment: RESIDUES 44-141
Source method: isolated from a genetically manipulated source
Details: CMI CLONED WITHOUT THE N-TERMINAL HYDROPHOBIC HELIX FOR EXPRESSION OF THE PROTEIN IN THE CYTOPLASM
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18002
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.26 Å3/Da / Density % sol: 45.65 % / Description: NONE
Crystal growDetails: 0.2 M AMMONIUM SULFATE, 30% PEG 4000

-
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: 1.89→50 Å / Num. obs: 15884 / % possible obs: 96.6 % / Observed criterion σ(I): 2.5 / Redundancy: 2.6 % / Biso Wilson estimate: 23.36 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11
Reflection shellResolution: 1.89→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 90

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: DIRECT METHODS
Starting model: ALPHA HELIX

Resolution: 1.892→28.224 Å / SU ML: 0.22 / σ(F): 2.03 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 434 5 %
Rwork0.2063 --
obs0.2072 8676 98.66 %
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.597 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.4534 Å20 Å20 Å2
2---2.1871 Å20 Å2
3---0.7337 Å2
Refinement stepCycle: LAST / Resolution: 1.892→28.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms746 0 5 54 805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011818
X-RAY DIFFRACTIONf_angle_d0.8781055
X-RAY DIFFRACTIONf_dihedral_angle_d15.403301
X-RAY DIFFRACTIONf_chiral_restr0.064107
X-RAY DIFFRACTIONf_plane_restr0.003137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8916-2.16520.29951390.23362651X-RAY DIFFRACTION97
2.1652-2.72760.23161450.19712757X-RAY DIFFRACTION100
2.7276-28.22670.20011500.20292834X-RAY DIFFRACTION99
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)
10.9803-0.37090.26951.208-0.22021.35210.0410.02630.0292-0.1931-0.008-0.15090.0503-0.04120.01460.0914-0.00090.00680.117-0.00260.099125.634155.40625.3832
22.55590.6785-0.2561.46720.32573.39510.0069-0.04680.1668-0.32390.07090.0664-0.06980.21410.01770.0269-0.0189-0.00120.07710.01020.053945.38957.73335.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 26:60)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 61:115)

+
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://pdbjlvh1.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