[English] 日本語
Yorodumi
- PDB-4cii: Crystal structure of N-terminally truncated Helicobacter pylori T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cii
TitleCrystal structure of N-terminally truncated Helicobacter pylori T4SS Protein CagL as domain swapped dimer
ComponentsCAG PATHOGENICITY ISLAND PROTEIN (CAG18)
KeywordsPROTEIN BINDING / ADHESION / RGD MOTIF / INTEGRIN BINDING / TYPE IV SECRETION / T4S / VIRULENCE / HP0539
Function / homologyCag pathogenicity island protein (Cag18)
Function and homology information
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBarden, S. / Schomburg, B. / Niemann, H.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure of a Three-Dimensional Domain-Swapped Dimer of the Helicobacter Pylori Type Iv Secretion System Pilus Protein Cagl.
Authors: Barden, S. / Schomburg, B. / Conradi, J. / Backert, S. / Sewald, N. / Niemann, H.H.
History
DepositionDec 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Experimental preparation / Other / Category: exptl_crystal_grow / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CAG PATHOGENICITY ISLAND PROTEIN (CAG18)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8652
Polymers25,7471
Non-polymers1181
Water82946
1
A: CAG PATHOGENICITY ISLAND PROTEIN (CAG18)
hetero molecules

A: CAG PATHOGENICITY ISLAND PROTEIN (CAG18)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7314
Polymers51,4942
Non-polymers2362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area6750 Å2
ΔGint-77.9 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.841, 61.841, 244.499
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2038-

HOH

-
Components

#1: Protein CAG PATHOGENICITY ISLAND PROTEIN (CAG18) / CAG PATHOGENICITY ISLAND PROTEIN 18


Mass: 25747.236 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-237
Source method: isolated from a genetically manipulated source
Details: FRAGMENT OF UNSPECIFIC N-TERMINAL PROTEOLYSIS OF CAGL(AA21-237)-LEHHHHHH IN THE CRYSTALLISATION DROP
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Plasmid: PET28-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: O25272
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINALLY (SIGNAL PEPTIDE) TRUNCATED CAGL (AA21-237) WITH A C-TERMINAL EXPRESSION TAG (LEHHHHHH)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.6 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 4.2
Details: 100 MM CITRATE/PHOSPHATE PH 4.2, 40% (V/V) 2-METHYL-2,4-PENTANEDIOL, 6.4% TERT-BUTANOL. VAPOR DIFFUSION AT 277 K WITH DROP RATIO OF 2:1 PROTEIN TO RESERVOIR.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→44.75 Å / Num. obs: 16080 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 30.24 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CZI

3czi


Resolution: 2.15→40.282 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 24.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 784 4.9 %
Rwork0.1985 --
obs0.2003 15977 99.69 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.67 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 8 46 1497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091512
X-RAY DIFFRACTIONf_angle_d0.9682035
X-RAY DIFFRACTIONf_dihedral_angle_d14.573593
X-RAY DIFFRACTIONf_chiral_restr0.069234
X-RAY DIFFRACTIONf_plane_restr0.003262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.28470.26211300.23652443X-RAY DIFFRACTION99
2.2847-2.46110.21761190.19662450X-RAY DIFFRACTION100
2.4611-2.70870.24571320.17292474X-RAY DIFFRACTION100
2.7087-3.10060.24231250.18212522X-RAY DIFFRACTION100
3.1006-3.90590.2231450.19122547X-RAY DIFFRACTION100
3.9059-40.28860.24241330.20892757X-RAY DIFFRACTION100
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)
14.26370.61291.46055.1948-0.0757.8466-0.0653-0.7160.16350.8129-0.2531-0.4199-0.63560.3070.12420.2348-0.066-0.06510.3011-0.00340.236724.2325-18.345527.9105
21.84020.02193.10843.1895-0.54375.2266-0.86740.22310.4924-0.7590.07530.0112-1.8959-0.03630.27740.7506-0.1711-0.21340.46810.11940.44059.7116-13.7497-8.8105
33.0180.5163.13150.8699-1.08549.1376-0.4431.00170.1313-0.33750.13530.10560.13181.2853-0.09190.2837-0.1333-0.05610.40830.0060.247717.833-22.37560.3047
41.2578-0.3984-2.12870.68290.38012.5687-0.0471-0.09240.1456-0.1238-0.0909-0.2418-0.2350.80510.14750.3188-0.12420.04850.3628-0.00810.265517.5803-23.306360.2615
52.9451.34182.64523.7973.16743.68120.1129-0.08670.04040.4544-0.14870.12221.183-0.0403-0.03980.3608-0.15940.03580.5036-0.12320.288520.2948-13.8897104.8281
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 61:90)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 91:125)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 126:178)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 179:208)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 209:240)

+
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