[English] 日本語
Yorodumi
- PDB-2yjl: Structural characterization of a secretin pilot protein from the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yjl
TitleStructural characterization of a secretin pilot protein from the type III secretion system (T3SS) of Pseudomonas aeruginosa
ComponentsEXOENZYME S SYNTHESIS PROTEIN B
KeywordsLIPID BINDING PROTEIN / LIPID-BINDING PROTEIN / PILOTIN
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Immunoglobulin-like - #2990 / : / Type 3 secretion system pilotin / Type III secretion system lipoprotein chaperone (YscW) / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Type 3 secretion system pilotin
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsIzore, T. / Perdu, C. / Job, V. / Atree, I. / Faudry, E. / Dessen, A.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Characterization and Membrane Localization of Exsb from the Type III Secretion System (T3Ss) of Pseudomonas Aeruginosa
Authors: Izore, T. / Perdu, C. / Job, V. / Atree, I. / Faudry, E. / Dessen, A.
History
DepositionMay 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EXOENZYME S SYNTHESIS PROTEIN B
B: EXOENZYME S SYNTHESIS PROTEIN B
C: EXOENZYME S SYNTHESIS PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8968
Polymers41,4533
Non-polymers4435
Water2,792155
1
A: EXOENZYME S SYNTHESIS PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0694
Polymers13,8181
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EXOENZYME S SYNTHESIS PROTEIN B


Theoretical massNumber of molelcules
Total (without water)13,8181
Polymers13,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: EXOENZYME S SYNTHESIS PROTEIN B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0103
Polymers13,8181
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.155, 48.358, 71.602
Angle α, β, γ (deg.)90.00, 96.92, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A20 - 131
2114B20 - 131
1214A160
2214B160
1316A151
2316B151
1124A20 - 131
2124C20 - 131
1224A160
2224C160
1326A151
2326C151

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.51225, 0.00762, -0.85881), (0.05636, 0.9981, -0.02476), (0.85699, -0.06109, -0.5117)33.57242, -16.06363, 20.68362
3given(-0.47304, 0.01893, 0.88084), (-0.01088, 0.99957, -0.02733), (-0.88097, -0.02251, -0.47263)-1.13611, -31.32739, 39.90014

-
Components

#1: Protein EXOENZYME S SYNTHESIS PROTEIN B / EXSB


Mass: 13817.702 Da / Num. of mol.: 3 / Fragment: RESIDUES 13-137
Source method: isolated from a genetically manipulated source
Details: SEQUENCE ENCOMPASSES RESIDUES 17-141 OF NATIVELY-EXPRESSED FULL-LENGTH PROTEIN
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA II / References: UniProt: P26994
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAN ALTERNATIVE START CODON WAS IDENTIFIED IN THIS STUDY, ADDING 4 AMINO TERMINAL RESIDUES TO THE ...AN ALTERNATIVE START CODON WAS IDENTIFIED IN THIS STUDY, ADDING 4 AMINO TERMINAL RESIDUES TO THE ANNOTATED SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 8.5
Details: TRIS 0.1 M PH 8.5, AMMONIUM SULFATE 1.5 M, GLYCEROL 10%.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.81→35 Å / Num. obs: 35870 / % possible obs: 90 % / Observed criterion σ(I): 3 / Redundancy: 3 % / Biso Wilson estimate: 28.825 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 29
Reflection shellResolution: 1.81→1.92 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 75.6

-
Processing

Software
NameVersionClassification
REFMAC5.6.0104refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.81→35.54 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.679 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26224 3463 9.9 %RANDOM
Rwork0.21691 ---
obs0.22138 31431 90.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20.55 Å2
2--0.27 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.81→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 21 155 2732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222783
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9643806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3285371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65120.647139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81915483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4741553
X-RAY DIFFRACTIONr_chiral_restr0.1110.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212147
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A768medium positional0.60.5
12B768medium positional0.60.5
21A798medium positional0.590.5
22C798medium positional0.590.5
21A5loose positional1.025
22C5loose positional1.025
11A768medium thermal3.982
12B768medium thermal3.982
21A798medium thermal2.822
22C798medium thermal2.822
21A5loose thermal6.7310
22C5loose thermal6.7310
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 170 -
Rwork0.406 1786 -
obs--69.29 %
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)
14.9657-0.71310.11911.02490.32211.0583-0.0957-0.06850.15990.05610.0438-0.1654-0.01120.04350.05190.04960.022-0.02150.0475-0.03220.0565-4.338719.393315.5935
22.2688-0.19641.53241.5701-0.17224.20630.0276-0.1117-0.04370.13680.01-0.0595-0.0716-0.0558-0.03760.1315-0.02630.03490.08140.01830.06115.1564-12.387935.9267
31.74190.2636-0.43381.7765-0.9893.0158-0.0866-0.0617-0.00610.06180.062-0.07910.07680.18570.02460.01160.0148-0.0010.0237-0.00040.030322.70853.79997.0457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 137
2X-RAY DIFFRACTION2C13 - 137
3X-RAY DIFFRACTION3B13 - 137

+
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