[English] 日本語
Yorodumi
- PDB-2hb0: Crystal Structure of CfaE, the Adhesive Subunit of CFA/I Fimbria ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hb0
TitleCrystal Structure of CfaE, the Adhesive Subunit of CFA/I Fimbria of Enterotoxigenic Escherichia coli
ComponentsCFA/I fimbrial subunit E
KeywordsCELL ADHESION / CfaE / Adhesin / ETEC / CFA/I / Traveler's Disease
Function / homology
Function and homology information


CFA/I fimbrial subunit E, adhesin domain / CblD-like pilus biogenesis initiator / CFA/I fimbrial subunit E, adhesin domain / CblD like pilus biogenesis initiator / CFA/I fimbrial subunit E, pilin domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MALONATE ION / DI(HYDROXYETHYL)ETHER / CFA/I fimbrial subunit E
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLi, Y.F. / Xia, D. / Poole, S. / Rasulova, F. / Savarino, S.J.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: A receptor-binding site as revealed by the crystal structure of CfaE, the colonization factor antigen I fimbrial adhesin of enterotoxigenic Escherichia coli.
Authors: Li, Y.F. / Poole, S. / Rasulova, F. / McVeigh, A.L. / Savarino, S.J. / Xia, D.
#1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Crystallization and preliminary X-ray diffraction analysis of CfaE, the adhesive subunit of the CFA/I fimbriae from human enterotoxigenic Escherichia coli.
Authors: Li, Y.F. / Poole, S. / Rasulova, F. / Esser, L. / Savarino, S.J. / Xia, D.
History
DepositionJun 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CFA/I fimbrial subunit E
B: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7099
Polymers81,9782
Non-polymers7317
Water11,962664
1
A: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4055
Polymers40,9891
Non-polymers4164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CFA/I fimbrial subunit E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3034
Polymers40,9891
Non-polymers3143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.346, 143.346, 231.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPLYSAA24 - 2012 - 179
21ASPLYSBB24 - 2012 - 179
32GLYSERAA202 - 374180 - 352
42GLYSERBB202 - 374180 - 352

-
Components

#1: Protein CFA/I fimbrial subunit E / Colonization factor antigen I subunit E


Mass: 40988.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cfaE / Production host: Escherichia coli (E. coli) / References: UniProt: P25734
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.61 %
Crystal growTemperature: 288 K / Method: vapor diffusion / pH: 7
Details: 10% PEGMME 550, 0.1M sodium HEPES, 1.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 63021 / % possible obs: 74.8 % / Rmerge(I) obs: 0.082

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.68 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20076 2460 4 %RANDOM
Rwork0.17783 ---
all0.227 ---
obs0.17874 58667 97.42 %-
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 mean: 25.447 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5517 0 21 692 6230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5191.9587688
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1273709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.216151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2110.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024276
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.32554
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.5914
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4380.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9711.53534
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87425719
X-RAY DIFFRACTIONr_scbond_it3.38132138
X-RAY DIFFRACTIONr_scangle_it5.2194.51969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1407tight positional0.170.05
1322loose positional0.445
1407tight thermal0.30.5
1322loose thermal210
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 146
Rwork0.263 3719
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)
11.7693-0.8893-1.22411.49311.17172.9256-0.0474-0.0376-0.2260.05830.0105-0.09970.41330.31960.03690.1450.07730.04350.1263-0.02460.134245.942718.372186.6876
23.481-0.4556-3.5791.16191.5335.2366-0.1034-0.2852-0.08560.2810.0090.05710.29110.17090.09440.17260.02150.04510.18650.02110.155914.617332.4116121.9503
31.1408-0.18861.08430.4758-0.07953.2694-0.01010.12880.0975-0.0113-0.0381-0.0796-0.18160.28680.04820.0405-0.0280.0560.0787-0.03390.077739.513141.370577.8217
41.77171.33661.54011.513.57227.32730.0187-0.08730.17690.14440.0496-0.0538-0.19930.2181-0.06830.238-0.0173-0.07740.2507-0.06850.304556.983253.8905122.1415
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 2012 - 179
2X-RAY DIFFRACTION2AA202 - 374180 - 352
3X-RAY DIFFRACTION3BB24 - 2012 - 179
4X-RAY DIFFRACTION4BB202 - 374180 - 352

+
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