[English] 日本語
Yorodumi
- PDB-6jqs: Structure of Transcription factor, GerE -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6jqs
TitleStructure of Transcription factor, GerE
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / GerE / spore
Biological speciesPaenisporosarcina sp. TG-14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.09 Å
AuthorsLee, J.H. / Lee, C.W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of a transcription factor, GerE (PaGerE), from spore-forming bacterium Paenisporosarcina sp. TG-14.
Authors: Lee, C.W. / Park, S.H. / Koh, H.Y. / Jeong, C.S. / Hwang, J. / Lee, S.G. / Youn, U.J. / Lee, C.S. / Park, H.H. / Kim, H.J. / Park, H. / Lee, J.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 1, 2019 / Release: Apr 24, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 24, 2019Structure modelrepositoryInitial release
1.1May 15, 2019Structure modelData collection / Database referencescitation_citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)8,6281
Polymers8,6281
Non-polymers00
Water72140
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)63.769, 63.769, 45.407
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-126-

HOH

-
Components

#1: Protein/peptide DNA-binding response regulator


Mass: 8627.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenisporosarcina sp. TG-14 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.18 M sodium chloride and 18% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.01→40 Å / % possible obs: 99.6 % / Redundancy: 7.1 % / Net I/σ(I): 35.3
Reflection shellResolution: 2.01→2.04 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MxDCdata collection
RefinementResolution: 2.09→21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.359 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25069 285 4.6 %RANDOM
Rwork0.20331 ---
Obs0.20562 5881 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.678 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.09→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms537 0 0 40 577
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0120.013539
r_bond_other_d0.0010.017551
r_angle_refined_deg1.8081.635721
r_angle_other_deg1.3571.5841271
r_dihedral_angle_1_deg6.314566
r_dihedral_angle_2_deg33.2352031
r_dihedral_angle_3_deg15.79615116
r_dihedral_angle_4_deg24.184157
r_chiral_restr0.0790.274
r_gen_planes_refined0.010.02581
r_gen_planes_other0.0010.02112
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it3.93.846267
r_mcbond_other3.9073.839266
r_mcangle_it4.4195.745332
r_mcangle_other4.4165.751333
r_scbond_it4.9334.478272
r_scbond_other4.8384.472270
r_scangle_it
r_scangle_other6.9246.48389
r_long_range_B_refined7.89845.327584
r_long_range_B_other7.88745.258582
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 29 -
Rwork0.182 427 -
Obs--98.06 %

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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