[English] 日本語
Yorodumi
- PDB-3mej: Crystal structure of putative transcriptional regulator ywtF from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mej
TitleCrystal structure of putative transcriptional regulator ywtF from Bacillus subtilis, Northeast Structural Genomics Consortium Target SR736
Componentstranscriptional regulator ywtF
Keywordstranscriptional regulator / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
Nucleotidyltransferase; domain 5 - #590 / LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagT
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.491 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target SR736
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMar 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: transcriptional regulator ywtF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3802
Polymers32,3451
Non-polymers351
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.210, 66.210, 141.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsmonomer,33.3 kD,90.5%

-
Components

#1: Protein transcriptional regulator ywtF


Mass: 32344.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU35840, ywtF / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7WY78
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: PEG3350 19%, MgCl 0.2M HEPES 7.5 10mM EDTA drop plate , VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97901 0.97925 0.96791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 25, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979251
30.967911
ReflectionResolution: 2.35→50 Å / Num. obs: 9933 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20.4 % / Rsym value: 0.087 / Net I/σ(I): 44.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 20 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 7.3 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
PHENIX1.5_2refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.491→44.458 Å / SU ML: 0.39 / σ(F): 1.68 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2703 990 9.97 %
Rwork0.2064 --
obs0.2126 9933 85.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL. / Bsol: 39.401 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso mean: 48.772 Å2
Refinement stepCycle: LAST / Resolution: 2.491→44.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1977 0 1 27 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092002
X-RAY DIFFRACTIONf_angle_d1.2382691
X-RAY DIFFRACTIONf_dihedral_angle_d21.92751
X-RAY DIFFRACTIONf_chiral_restr0.075313
X-RAY DIFFRACTIONf_plane_restr0.005342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4907-2.6220.2749950.2152914X-RAY DIFFRACTION62
2.622-2.78620.33781180.22871091X-RAY DIFFRACTION74
2.7862-3.00130.2881360.23721208X-RAY DIFFRACTION83
3.0013-3.30330.3261470.22251320X-RAY DIFFRACTION89
3.3033-3.7810.27451550.2031386X-RAY DIFFRACTION93
3.781-4.76280.2271640.16891472X-RAY DIFFRACTION97
4.7628-44.46480.25021750.20511552X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 19.8252 Å / Origin y: 43.4355 Å / Origin z: 66.773 Å
111213212223313233
T0.1331 Å2-0.0036 Å2-0.0027 Å2-0.2062 Å20.0049 Å2--0.1726 Å2
L1.2686 °2-0.2504 °20.7826 °2-0.6085 °2-0.358 °2--0.6888 °2
S-0.0486 Å °-0.1493 Å °-0.0088 Å °0.0243 Å °0.0032 Å °0.0002 Å °-0.0357 Å °-0.0462 Å °0.0399 Å °
Refinement TLS groupSelection details: all

+
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