[English] 日本語
Yorodumi
- PDB-3gr5: Periplasmic domain of the outer membrane secretin EscC from enter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gr5
TitlePeriplasmic domain of the outer membrane secretin EscC from enteropathogenic E.coli (EPEC)
ComponentsEscC
KeywordsMEMBRANE PROTEIN / secretin / Type III secretion system / outer membrane / Transport
Function / homology
Function and homology information


protein secretion / cell outer membrane
Similarity search - Function
Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system ...Ribosomal Protein S8; Chain: A, domain 1 - #120 / Phage tail protein beta-alpha-beta fold - #30 / Phage tail protein beta-alpha-beta fold / Type III secretion system outer membrane pore YscC/HrcC / Bacterial type II secretion system protein D signature. / Type II secretion system protein GspD, conserved site / NolW-like / Bacterial type II/III secretion system short domain / NolW-like superfamily / Type II/III secretion system / Bacterial type II and III secretion system protein / 3-Layer(bab) Sandwich / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Type 3 secretion system secretin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsYip, C.K. / Vockovic, M. / Strynadka, N.C.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2009
Title: A conserved structural motif mediates formation of the periplasmic rings in the type III secretion system.
Authors: Spreter, T. / Yip, C.K. / Sanowar, S. / Andre, I. / Kimbrough, T.G. / Vuckovic, M. / Pfuetzner, R.A. / Deng, W. / Yu, A.C. / Finlay, B.B. / Baker, D. / Miller, S.I. / Strynadka, N.C.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EscC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1454
Polymers17,8571
Non-polymers2883
Water1,38777
1
A: EscC
hetero molecules

A: EscC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2918
Polymers35,7152
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3320 Å2
ΔGint-73 kcal/mol
Surface area15520 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.645, 90.645, 133.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

-
Components

#1: Protein EscC


Mass: 17857.307 Da / Num. of mol.: 1 / Fragment: EscC periplasmic domain, residues 21-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: escC / Production host: Escherichia coli (E. coli) / References: UniProt: O52135
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 4.43 Å3/Da / Density % sol: 72.24 %
Crystal growDetails: microbatch, 2.0 M Ammonium sulfate + 0.1 M sodium acetate pH 4.5 or Bis-Tris pH 6.5

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→18.7 Å / Num. obs: 20942 / % possible obs: 100 %

-
Processing

Software
NameVersionClassificationNB
REFMAC5.1.24refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.05→18.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.57 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1072 5.1 %RANDOM
Rwork0.213 ---
obs0.215 20941 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 104.46 Å2 / Biso mean: 42.164 Å2 / Biso min: 19.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.05→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 15 77 1329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0221272
X-RAY DIFFRACTIONr_bond_other_d0.0020.021144
X-RAY DIFFRACTIONr_angle_refined_deg2.1021.9841722
X-RAY DIFFRACTIONr_angle_other_deg0.98332686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765152
X-RAY DIFFRACTIONr_chiral_restr0.1420.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021353
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02239
X-RAY DIFFRACTIONr_nbd_refined0.2310.2279
X-RAY DIFFRACTIONr_nbd_other0.2510.21310
X-RAY DIFFRACTIONr_nbtor_other0.0920.2722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3140.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3140.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2930.24
X-RAY DIFFRACTIONr_mcbond_it1.7631.5767
X-RAY DIFFRACTIONr_mcangle_it3.24221259
X-RAY DIFFRACTIONr_scbond_it4.3553505
X-RAY DIFFRACTIONr_scangle_it7.1984.5463
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.286 88
Rwork0.248 1433
all-1521

+
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