[English] 日本語
Yorodumi
- PDB-3uu2: Salmonella typhi osmoporin(OmpC):an Outer Membrane Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uu2
TitleSalmonella typhi osmoporin(OmpC):an Outer Membrane Protein
ComponentsOuter membrane protein C
KeywordsMEMBRANE PROTEIN / Beta Barrel / Non specific porin / osmoporin / Outer Membrane
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin C / Outer membrane porin C
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsPrasanth, P. / Putcha, B.K. / Arockiasamy, A. / Krishnaswamy, S.
CitationJournal: To be Published
Title: Crystal Structure of Outer membrane protein OmpC from Salmonella typhi.
Authors: Prasanth, P. / Putcha, B.K. / Arockiasamy, A. / Krishnaswamy, S.
History
DepositionNov 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer membrane protein C
B: Outer membrane protein C
C: Outer membrane protein C


Theoretical massNumber of molelcules
Total (without water)117,6213
Polymers117,6213
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-57 kcal/mol
Surface area39660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.201, 108.568, 113.391
Angle α, β, γ (deg.)90.00, 117.83, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Outer membrane protein C / Porin ompC


Mass: 39207.059 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: Ty21a / Gene: ompC, STM2267 / Plasmid: pET21b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A263, UniProt: P0A264*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 70.83 %
Crystal growTemperature: 298.15 K / Method: microbatch under oil / pH: 8.5
Details: 0.01M Nickel(II) chloride hexahydrate, 0.1M Tris, 20% PEG MME 2000, pH 8.5, Microbatch under oil, temperature 298.15K

-
Data collection

DiffractionMean temperature: 77.03 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.0048 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0048 Å / Relative weight: 1
ReflectionResolution: 3.33→100.27 Å / Num. all: 28544 / Num. obs: 27261 / % possible obs: 95.7 % / Redundancy: 12.1 % / Biso Wilson estimate: 97.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 23
Reflection shellResolution: 3.59→3.67 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 2.95 / % possible all: 93.2

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UPG

3upg


Resolution: 3.59→50 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.848 / SU B: 130.247 / SU ML: 0.857 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R Free: 0.748 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.35808 1170 5.1 %RANDOM
Rwork0.30196 ---
obs0.3049 21573 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 225.198 Å2
Baniso -1Baniso -2Baniso -3
1-4.96 Å20 Å2-1.66 Å2
2--7.52 Å20 Å2
3----14.02 Å2
Refinement stepCycle: LAST / Resolution: 3.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6988 0 0 0 6988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227144
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9269663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4215882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.13725.076396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.251151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8051521
X-RAY DIFFRACTIONr_chiral_restr0.1050.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025739
X-RAY DIFFRACTIONr_mcbond_it0.5711.54341
X-RAY DIFFRACTIONr_mcangle_it1.10426843
X-RAY DIFFRACTIONr_scbond_it1.1532803
X-RAY DIFFRACTIONr_scangle_it1.9974.52820
LS refinement shellResolution: 3.59→3.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 80 -
Rwork0.376 1492 -
obs--93.63 %
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)
17.5299-1.5963-3.75594.6944-0.215213.0688-1.33391.2656-1.8558-0.7128-0.1781-0.04671.8538-0.71251.51210.6887-0.3760.38390.5287-0.44590.7645-20.1194-42.878425.1783
25.72010.2118-3.68924.4353-1.30378.43280.9894-0.2960.6286-0.2053-0.2135-0.738-3.46992.7482-0.77591.7876-1.35270.29811.3591-0.33250.5842-1.3387-9.6130.0583
34.82571.0771-1.60633.6957-0.48016.55540.71931.82820.5995-0.8199-0.12060.6219-3.3187-2.4214-0.59872.10881.24230.05421.98050.42070.4828-38.0577-9.277420.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 357
2X-RAY DIFFRACTION2B1 - 357
3X-RAY DIFFRACTION3C1 - 357

+
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