[English] 日本語
Yorodumi
- PDB-3vor: Crystal Structure Analysis of the CofA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vor
TitleCrystal Structure Analysis of the CofA
ComponentsCFA/III pilin
KeywordsCELL ADHESION / Type IV pilin / colonization
Function / homology
Function and homology information


extracellular organelle / pilus / membrane
Similarity search - Function
TcpA-like pilin / TcpA-like pilin / Toxin-coregulated pilus subunit TcpA / Toxin-coregulated pilus subunit TcpA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.9 Å
AuthorsFukakusa, S. / Kawahara, K. / Nakamura, S. / Iwasita, T. / Baba, S. / Nishimura, M. / Kobayashi, Y. / Honda, T. / Iida, T. / Taniguchi, T. / Ohkubo, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure of the CFA/III major pilin subunit CofA from human enterotoxigenic Escherichia coli determined at 0.90 A resolution by sulfur-SAD phasing
Authors: Fukakusa, S. / Kawahara, K. / Nakamura, S. / Iwashita, T. / Baba, S. / Nishimura, M. / Kobayashi, Y. / Honda, T. / Iida, T. / Taniguchi, T. / Ohkubo, T.
History
DepositionFeb 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CFA/III pilin


Theoretical massNumber of molelcules
Total (without water)18,9001
Polymers18,9001
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.820, 47.710, 42.450
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CFA/III pilin / CofA / Major pilin subunit


Mass: 18899.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: 260-1 / Gene: cofA / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: Q59393
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.73 Å3/Da / Density % sol: 28.8 %
Crystal growTemperature: 293 K / pH: 3.8
Details: 26% PEG 4000, pH 3.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2011
RadiationMonochromator: SI (111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionRedundancy: 13.2 % / Av σ(I) over netI: 0 / Number: 351095 / Rmerge(I) obs: 0.051 / Χ2: 2.1 / D res high: 0.9 Å / D res low: 30.86 Å / Num. obs: 26512 / % possible obs: 96.4
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
3.7550110196.20.0362.14513.4
2.973.75196699.60.0372.2814.5
2.62.9725411000.0412.38814.8
2.362.629711000.0462.41113.2
2.192.36337299.90.0492.5413.5
2.062.19370299.80.0552.88413.6
1.962.06397199.80.0612.98413.5
1.871.96420299.90.0662.87813.5
1.81.87443799.90.0682.56513.6
1.741.845861000.0722.15713.6
1.681.7447641000.0772.01213.6
1.641.6849831000.0821.90313.6
1.591.6452241000.091.77513.4
1.551.5954401000.0941.7413.4
1.521.5556121000.1071.62813.4
1.491.5258381000.1191.50713.1
1.461.4959841000.1391.37913.1
1.431.4662381000.1591.36612.9
1.41.43638699.80.1961.46312.4
1.381.4656297.10.2481.5628.6
ReflectionResolution: 0.9→30.86 Å / Num. obs: 91809 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 3.2 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.6
Reflection shellResolution: 0.9→0.95 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 7.11 / % possible all: 94.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 0.9→30.86 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.08 / σ(F): 1.35 / Phase error: 9.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.13 4590 5 %
Rwork0.12 --
obs0.121 91733 96.4 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.895 Å2 / ksol: 0.558 e/Å3
Displacement parametersBiso mean: 4.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.1894 Å20 Å20.0028 Å2
2--0.7523 Å20 Å2
3---0.4371 Å2
Refinement stepCycle: LAST / Resolution: 0.9→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 0 237 1559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091611
X-RAY DIFFRACTIONf_angle_d1.5412216
X-RAY DIFFRACTIONf_dihedral_angle_d13.484636
X-RAY DIFFRACTIONf_chiral_restr0.086263
X-RAY DIFFRACTIONf_plane_restr0.009299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.91020.15821500.14582850X-RAY DIFFRACTION95
0.9102-0.92090.15921480.13942831X-RAY DIFFRACTION95
0.9209-0.93220.13411500.13242843X-RAY DIFFRACTION95
0.9322-0.9440.13421530.12832899X-RAY DIFFRACTION95
0.944-0.95640.12781480.12092825X-RAY DIFFRACTION95
0.9564-0.96950.12541520.11972884X-RAY DIFFRACTION95
0.9695-0.98340.11631500.11482841X-RAY DIFFRACTION96
0.9834-0.9980.11111510.10732868X-RAY DIFFRACTION95
0.998-1.01360.10841530.10662903X-RAY DIFFRACTION96
1.0136-1.03030.10171510.09972875X-RAY DIFFRACTION96
1.0303-1.0480.11961520.10172883X-RAY DIFFRACTION96
1.048-1.06710.11441520.12895X-RAY DIFFRACTION96
1.0671-1.08760.10951530.0932897X-RAY DIFFRACTION96
1.0876-1.10980.09021510.08952874X-RAY DIFFRACTION96
1.1098-1.13390.08151520.08572894X-RAY DIFFRACTION96
1.1339-1.16030.09681530.08372898X-RAY DIFFRACTION96
1.1603-1.18930.11661510.08822876X-RAY DIFFRACTION96
1.1893-1.22150.09741540.0882933X-RAY DIFFRACTION97
1.2215-1.25740.10221540.09322917X-RAY DIFFRACTION97
1.2574-1.2980.10961540.09882916X-RAY DIFFRACTION97
1.298-1.34440.10091530.09752911X-RAY DIFFRACTION97
1.3444-1.39820.12551540.10382924X-RAY DIFFRACTION97
1.3982-1.46190.12041550.10162957X-RAY DIFFRACTION97
1.4619-1.53890.13761550.10842942X-RAY DIFFRACTION97
1.5389-1.63540.11711550.1122941X-RAY DIFFRACTION97
1.6354-1.76160.14011560.12212960X-RAY DIFFRACTION98
1.7616-1.93890.13251550.12892944X-RAY DIFFRACTION98
1.9389-2.21940.15191560.13022967X-RAY DIFFRACTION98
2.2194-2.79590.1541580.14222994X-RAY DIFFRACTION98
2.7959-30.88320.17681610.18043041X-RAY DIFFRACTION98

+
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