[English] 日本語
Yorodumi
- PDB-3tlq: Crystal structure of EAL-like domain protein YdiV -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tlq
TitleCrystal structure of EAL-like domain protein YdiV
ComponentsRegulatory protein YdiV
KeywordsTRANSCRIPTION / Anti-Flhd4c2 factor / Repress motility
Function / homology
Function and homology information


regulation of single-species biofilm formation / negative regulation of bacterial-type flagellum-dependent cell motility / cyclic-guanylate-specific phosphodiesterase activity / plasma membrane
Similarity search - Function
EAL domain / : / EAL domain / EAL domain superfamily / EAL domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Putative anti-FlhC(2)FlhD(4) factor YdiV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsLi, B. / Li, N. / Wang, F. / Guo, L. / Liu, C. / Zhu, D. / Xu, S. / Gu, L.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility
Authors: Li, B. / Li, N. / Wang, F. / Guo, L. / Huang, Y. / Liu, X. / Wei, T. / Zhu, D. / Liu, C. / Pan, H. / Xu, S. / Wang, H.W. / Gu, L.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Jul 3, 2013Group: Database references / Other
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Regulatory protein YdiV
B: Regulatory protein YdiV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,80911
Polymers54,9632
Non-polymers8469
Water7,044391
1
A: Regulatory protein YdiV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2339
Polymers27,4821
Non-polymers7518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Regulatory protein YdiV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5772
Polymers27,4821
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.576, 50.348, 111.072
Angle α, β, γ (deg.)90.00, 98.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Regulatory protein YdiV / EAL-like domain protein YdiV


Mass: 27481.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MG1655 / Gene: b1707, JW1697, ydiV / Plasmid: pGL01 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76204
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 2.0M Sodium/Potassium phosphate PH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 41951 / Num. obs: 41951 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.14 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.91-1.9830.1975.4839370.19794.1
4.11-503.60.05325.5343730.05399.6

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.91→39.635 Å / SU ML: 0.19 / σ(F): 0 / σ(I): 0 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2004 1940 4.75 %RANDOM
Rwork0.1718 ---
all0.1732 40814 --
obs0.1732 40814 96.2 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.925 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso mean: 15.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.5628 Å20 Å20.0883 Å2
2--2.4489 Å2-0 Å2
3----0.8861 Å2
Refinement stepCycle: LAST / Resolution: 1.91→39.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3791 0 48 391 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073927
X-RAY DIFFRACTIONf_angle_d1.0765343
X-RAY DIFFRACTIONf_dihedral_angle_d14.5391428
X-RAY DIFFRACTIONf_chiral_restr0.076604
X-RAY DIFFRACTIONf_plane_restr0.005685
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9087-1.95640.24031190.1909248788
1.9564-2.00930.20911320.1603264592
2.0093-2.06850.18861460.1607267793
2.0685-2.13520.21211260.157271895
2.1352-2.21150.19271320.1553276096
2.2115-2.30010.21231470.151273796
2.3001-2.40470.19241390.1621275396
2.4047-2.53150.21031420.1747281297
2.5315-2.69010.23041400.1776280298
2.6901-2.89770.1891410.1737286099
2.8977-3.18920.18961380.1703288499
3.1892-3.65040.19921430.1641285699
3.6504-4.5980.17111480.1613293299
4.598-39.64360.21931470.2175295199

+
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