[English] 日本語
Yorodumi
- PDB-1p9h: CRYSTAL STRUCTURE OF THE COLLAGEN-BINDING DOMAIN OF YERSINIA ADHE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1p9h
TitleCRYSTAL STRUCTURE OF THE COLLAGEN-BINDING DOMAIN OF YERSINIA ADHESIN YadA
ComponentsInvasin
KeywordsCELL ADHESION / collagen-binding / left-handed beta-roll
Function / homology
Function and homology information


protein secretion by the type V secretion system / collagen binding / cell outer membrane / cell adhesion / cell surface
Similarity search - Function
Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain ...Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal / Mainly Beta
Similarity search - Domain/homology
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsNummelin, H. / Merckel, M.C. / Skurnik, M. / Goldman, A.
CitationJournal: Embo J. / Year: 2004
Title: The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.
Authors: Nummelin, H. / Merckel, M.C. / Leo, J.C. / Lankinen, H. / Skurnik, M. / Goldman, A.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Invasin


Theoretical massNumber of molelcules
Total (without water)22,8061
Polymers22,8061
Non-polymers00
Water1,892105
1
A: Invasin

A: Invasin

A: Invasin


Theoretical massNumber of molelcules
Total (without water)68,4183
Polymers68,4183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area15080 Å2
ΔGint-95 kcal/mol
Surface area16840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.050, 67.050, 221.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Invasin / Outer membrane adhesin


Mass: 22806.059 Da / Num. of mol.: 1 / Fragment: COLLAGEN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: YADA OR YOPA OR INVA OR YOP1 / Plasmid: pHN-1 / Production host: Escherichia coli (E. coli) / Strain (production host): M15(pREP4) / References: UniProt: P31489
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, sodium acetate, sodium-cacotylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 %PEG80001reservoir
20.2 Msodium acetate1reservoir
30.1 MTris-HCl1reservoirpH6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9102 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. all: 28431 / Num. obs: 28240 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 24
Reflection shellResolution: 1.55→1.61 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.5 / Num. unique all: 2763 / % possible all: 99.4
Reflection
*PLUS
Num. obs: 32335 / % possible obs: 99.8 % / Num. measured all: 355936 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 99.4 % / Num. unique obs: 2683

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→19.87 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 263358.66 / Data cutoff high rms absF: 263358.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 2694 9.9 %RANDOM
Rwork0.1956 ---
all-28429 --
obs-27177 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 124.626 Å2 / ksol: 0.704203 e/Å3
Displacement parametersBiso mean: 17 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.62 Å20 Å2
2--0.31 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.55→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1228 0 0 105 1333
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.66
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.275 417 10.2 %
Rwork0.233 3665 -
obs--87.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 23731 / Num. reflection Rfree: 2569 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.384
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.66

+
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