[English] 日本語
Yorodumi
- PDB-3h7z: A transition from strong right-handed to canonical left-handed su... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h7z
TitleA transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled coil segment of trimeric autotransporter adhesins - the M1 mutant structure
ComponentsAdhesin yadA
KeywordsCELL ADHESION / YadA / Adhesion / Adhesin / Coiled coil / Mutant / Cell membrane / Cell outer membrane / Membrane / Plasmid / Virulence
Function / homology
Function and homology information


collagen binding / cell outer membrane / protein transport / cell adhesion / cell surface
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2280 / Outer membrane adhesion, Yersinia / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsZeth, K. / Hernandez-Alvarez, B. / Lupas, A.N.
CitationJournal: J.Struct.Biol. / Year: 2010
Title: A transition from strong right-handed to canonical left-handed supercoiling in a conserved coiled-coil segment of trimeric autotransporter adhesins.
Authors: Alvarez, B.H. / Gruber, M. / Ursinus, A. / Dunin-Horkawicz, S. / Lupas, A.N. / Zeth, K.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)6,9131
Polymers6,9131
Non-polymers00
Water1267
1
A: Adhesin yadA

A: Adhesin yadA

A: Adhesin yadA


Theoretical massNumber of molelcules
Total (without water)20,7383
Polymers20,7383
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6630 Å2
ΔGint-58 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.896, 31.896, 147.864
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein Adhesin yadA


Mass: 6912.774 Da / Num. of mol.: 1 / Fragment: YadA stalk domain structure mutant M1 / Mutation: V349L, D350L, G352L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: yadA / Production host: Escherichia coli (E. coli) / References: UniProt: P0C2W0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% Peg3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.457
11-H-K, K, -L20.543
ReflectionResolution: 2.5→30 Å / Num. obs: 2590 / % possible obs: 91 % / Observed criterion σ(I): 12 / Redundancy: 2.6 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.003 / Rsym value: 0.003 / Net I/σ(I): 26.3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 12 / Num. unique all: 875 / Rsym value: 0.007

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0063refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD MODEL

Resolution: 2.51→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.894 / SU B: 16.41 / SU ML: 0.344 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27894 136 4.9 %RANDOM
Rwork0.2327 ---
obs0.23507 2590 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.298 Å2
Baniso -1Baniso -2Baniso -3
1-17.57 Å20 Å20 Å2
2--17.57 Å20 Å2
3----35.14 Å2
Refinement stepCycle: LAST / Resolution: 2.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms485 0 0 7 492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021490
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.961661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.74424.54522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.2831595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.26153
X-RAY DIFFRACTIONr_chiral_restr0.1040.282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02348
X-RAY DIFFRACTIONr_mcbond_it0.5871.5304
X-RAY DIFFRACTIONr_mcangle_it1.1522490
X-RAY DIFFRACTIONr_scbond_it1.5833186
X-RAY DIFFRACTIONr_scangle_it2.6754.5171
LS refinement shellResolution: 2.51→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 17 -
Rwork0.282 172 -
obs--92.2 %

+
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