[English] 日本語
Yorodumi
- PDB-5fr7: Erwinia amylovora AmyR amylovoran repressor, a member of the YbjN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fr7
TitleErwinia amylovora AmyR amylovoran repressor, a member of the YbjN protein family
ComponentsAMYR
KeywordsSIGNALING PROTEIN / AMYLOVORAN / YBJN / FIRE BLIGHT / PLANT PATHOGEN / T3SS
Function / homologyPutative sensory transduction regulator YbjN / Putative bacterial sensory transduction regulator / Uncharacterized protein ybjN
Function and homology information
Biological speciesERWINIA AMYLOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Walsh, M. / Benini, S.
CitationJournal: PLoS ONE / Year: 2017
Title: The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions.
Authors: Bartho, J.D. / Bellini, D. / Wuerges, J. / Demitri, N. / Toccafondi, M. / Schmitt, A.O. / Zhao, Y. / Walsh, M.A. / Benini, S.
History
DepositionDec 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMYR
B: AMYR


Theoretical massNumber of molelcules
Total (without water)36,0862
Polymers36,0862
Non-polymers00
Water1,65792
1
A: AMYR
B: AMYR

A: AMYR
B: AMYR


Theoretical massNumber of molelcules
Total (without water)72,1714
Polymers72,1714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area7590 Å2
ΔGint-58.5 kcal/mol
Surface area25930 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-20.2 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.163, 49.816, 57.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein AMYR / PROTEIN YBJN


Mass: 18042.807 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA AMYLOVORA (bacteria) / Strain: CFBP1430 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D4I047
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL GA ADDED FROM TEV PROTEASE CLEAVAGE SITE. H2G MUTATION A CLONING ARTEFACT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.12 % / Description: NONE
Crystal growpH: 6.9
Details: 0.1M SODIUM CACODYLATE PH 6.9, 0.2M MAGNESIUM CHLORIDE, 46% (V/V) PEG200

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.95→53.26 Å / Num. obs: 29587 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.14 Å / Redundancy: 5 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPDB ENTRY 5FRK

5frk


Resolution: 1.95→53.26 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.423 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY OLIGOMERIC STATE IS UNCERTAIN
RfactorNum. reflection% reflectionSelection details
Rfree0.26863 1439 4.9 %RANDOM
Rwork0.2236 ---
obs0.22588 28002 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.392 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.86 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→53.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2238 0 0 92 2330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192282
X-RAY DIFFRACTIONr_bond_other_d0.0010.022213
X-RAY DIFFRACTIONr_angle_refined_deg1.7971.9633099
X-RAY DIFFRACTIONr_angle_other_deg0.8563.0025089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.97526.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.64815396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.725153
X-RAY DIFFRACTIONr_chiral_restr0.110.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
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
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 93 -
Rwork0.34 2039 -
obs--98.7 %

+
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