[English] 日本語
Yorodumi
- PDB-2uy7: Crystal structure of the P pilus rod subunit PapA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uy7
TitleCrystal structure of the P pilus rod subunit PapA
Components
  • PAP FIMBRIAL MAJOR PILIN PROTEIN
  • PERIPLASMID CHAPERONE PAPD PROTEIN
KeywordsCHAPERONE / DONOR STRAND COMPLEMENTATION / PILI/N-TERMINAL EXTENSION / PILUS BIOGENESIS / DONOR-STRAND EXCHANGE / NTE / DSC / DSE / PAPA / PAPD / FIMBRIA
Function / homology
Function and homology information


cell adhesion involved in single-species biofilm formation / pilus / : / cell wall organization / outer membrane-bounded periplasmic space / extracellular region
Similarity search - Function
Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily ...Pili assembly chaperone, C-terminal / Pili assembly chaperone PapD, C-terminal domain / Pili assembly chaperone, bacterial / Pili assembly chaperone, conserved site / Pili assembly chaperone, C-terminal domain superfamily / Gram-negative pili assembly chaperone signature. / Pili assembly chaperone, N-terminal / : / Pili and flagellar-assembly chaperone, PapD N-terminal domain / PapD-like superfamily / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pap fimbrial major pilin protein / Periplasmid chaperone PapD protein
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVerger, D. / Bullitt, E. / Hultgren, S.J. / Waksman, G.
CitationJournal: Plos Pathog. / Year: 2007
Title: Crystal Structure of the P Pilus Rod Subunit Papa.
Authors: Verger, D. / Bullitt, E. / Hultgren, S.J. / Waksman, G.
History
DepositionApr 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PERIPLASMID CHAPERONE PAPD PROTEIN
B: PAP FIMBRIAL MAJOR PILIN PROTEIN
C: PERIPLASMID CHAPERONE PAPD PROTEIN
D: PAP FIMBRIAL MAJOR PILIN PROTEIN
E: PERIPLASMID CHAPERONE PAPD PROTEIN
F: PAP FIMBRIAL MAJOR PILIN PROTEIN
G: PERIPLASMID CHAPERONE PAPD PROTEIN
H: PAP FIMBRIAL MAJOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,11021
Polymers164,8618
Non-polymers1,24913
Water4,179232
1
A: PERIPLASMID CHAPERONE PAPD PROTEIN
B: PAP FIMBRIAL MAJOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6967
Polymers41,2152
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PERIPLASMID CHAPERONE PAPD PROTEIN
D: PAP FIMBRIAL MAJOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5035
Polymers41,2152
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: PERIPLASMID CHAPERONE PAPD PROTEIN
F: PAP FIMBRIAL MAJOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3113
Polymers41,2152
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: PERIPLASMID CHAPERONE PAPD PROTEIN
H: PAP FIMBRIAL MAJOR PILIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6006
Polymers41,2152
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)166.960, 166.960, 178.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein
PERIPLASMID CHAPERONE PAPD PROTEIN


Mass: 24589.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: WILD TYPE P PILUS CHAPERONE PAPD / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: UTI89 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: Q1R2W9
#2: Protein
PAP FIMBRIAL MAJOR PILIN PROTEIN / PAP PILI


Mass: 16625.396 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: P PILUS ROD SUBUNIT PAPA / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: J96 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C600 / References: UniProt: P04127
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLY 37 TO ASN ...ENGINEERED RESIDUE IN CHAIN B, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN D, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN F, GLY 37 TO ASN ENGINEERED RESIDUE IN CHAIN H, GLY 37 TO ASN
Has protein modificationY
Sequence detailsMATURE PROTEIN SEQUENCE AFTER CLIVAGE OF SIGNAL SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.24 Å3/Da / Density % sol: 71 %
Crystal growpH: 5.6 / Details: 2M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH = 5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→75.8 Å / Num. obs: 88336 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDK

1pdk


Resolution: 2.6→75.8 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE 4 COMPLEXES IN THE ASYMETRIC UNIT WERE RETRAINED BY NCS, USING THE MOST SIMILAR PARTS OF THE CORE STRUCTURE (MAIN CHAIN)
RfactorNum. reflection% reflectionSelection details
Rfree0.266 4417 5 %RANDOM
Rwork0.2296 ---
obs0.2296 88123 99.7 %-
Solvent computationBsol: 38.4771 Å2 / ksol: 0.36868 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→75.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11030 0 65 232 11327
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006528
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35371
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.387 --
Rwork0.378 1682 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

+
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