[English] 日本語
Yorodumi
- PDB-5kol: Crystal structure of the competence-damaged protein (CinA) superf... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5kol
TitleCrystal structure of the competence-damaged protein (CinA) superfamily protein ECK1530/EC0983 from Escherichia coli
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CinA / Competence-damaged protein / outer membrane biogenesis / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Disease
Function / homology
Function and homology information


CinA-like / CinA, C-terminal / CinA-like, C-terminal / : / Competence-damaged protein / Maf protein / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Inactive PncC family protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsStogios, P.J. / Wawrak, Z. / Evdokimova, E. / Di Leo, R. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: To be published
Authors: Stogios, P.J.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6778
Polymers73,4554
Non-polymers2224
Water12,160675
1
A: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8554
Polymers36,7282
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-22 kcal/mol
Surface area15600 Å2
MethodPISA
2
B: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8224
Polymers36,7282
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-23 kcal/mol
Surface area15900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.690, 89.150, 245.220
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
11B-202-

ACT

21B-202-

ACT

31B-322-

HOH

41D-221-

HOH

-
Components

#1: Protein
Uncharacterized protein


Mass: 18363.760 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: ydeJ, ECs2146, Z2161 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8XB29
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5 M ammonium chloride, 0.1 M sodium acetate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.91→37.885 Å / Num. obs: 65002 / % possible obs: 99.2 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 16.1
Reflection shellResolution: 1.91→1.96 Å / Redundancy: 6 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.838 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PHENIXphasing
HKL-3000data scaling
Cootmodel building
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A9S

2a9s


Resolution: 1.91→37.885 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2511 3302 5.1 %RANDOM
Rwork0.2065 ---
obs0.2088 64773 98.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.91→37.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5140 0 12 678 5830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075282
X-RAY DIFFRACTIONf_angle_d0.8377177
X-RAY DIFFRACTIONf_dihedral_angle_d19.6831888
X-RAY DIFFRACTIONf_chiral_restr0.054850
X-RAY DIFFRACTIONf_plane_restr0.004931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93730.61171260.55112351X-RAY DIFFRACTION92
1.9373-1.96620.39951340.40222423X-RAY DIFFRACTION94
1.9662-1.99690.35111170.31422521X-RAY DIFFRACTION100
1.9969-2.02970.31691200.28562638X-RAY DIFFRACTION100
2.0297-2.06470.31781400.28522516X-RAY DIFFRACTION100
2.0647-2.10220.3481520.27642570X-RAY DIFFRACTION100
2.1022-2.14270.30361350.26152555X-RAY DIFFRACTION100
2.1427-2.18640.28181360.2522597X-RAY DIFFRACTION100
2.1864-2.23390.31071330.27882500X-RAY DIFFRACTION98
2.2339-2.28590.41191400.35272361X-RAY DIFFRACTION92
2.2859-2.3430.28691480.24632570X-RAY DIFFRACTION100
2.343-2.40640.2841540.23182540X-RAY DIFFRACTION100
2.4064-2.47720.27781350.21582579X-RAY DIFFRACTION100
2.4772-2.55710.2581580.21662584X-RAY DIFFRACTION100
2.5571-2.64850.28521140.21352576X-RAY DIFFRACTION100
2.6485-2.75450.28661340.21472577X-RAY DIFFRACTION100
2.7545-2.87980.23911340.20992586X-RAY DIFFRACTION100
2.8798-3.03160.28911420.20782596X-RAY DIFFRACTION100
3.0316-3.22140.23221440.2042597X-RAY DIFFRACTION100
3.2214-3.470.26021350.18992622X-RAY DIFFRACTION100
3.47-3.81890.21841390.17372588X-RAY DIFFRACTION100
3.8189-4.37080.20191320.15082632X-RAY DIFFRACTION100
4.3708-5.50410.15771330.14982680X-RAY DIFFRACTION100
5.5041-37.89210.19661670.16762712X-RAY DIFFRACTION99

+
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