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- PDB-6jqs: Structure of Transcription factor, GerE -

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Basic information

Entry
Database: PDB / ID: 6jqs
TitleStructure of Transcription factor, GerE
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / GerE / spore
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
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.
History
DepositionApr 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator


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


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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

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Components

#1: Protein 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) / References: UniProt: A0A4V8H024*PLUS
#2: Water ChemComp-HOH / water / Water


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

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Experimental details

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Experiment

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

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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

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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

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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
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013539
X-RAY DIFFRACTIONr_bond_other_d0.0010.017551
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.635721
X-RAY DIFFRACTIONr_angle_other_deg1.3571.5841271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.314566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2352031
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.79615116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.184157
X-RAY DIFFRACTIONr_chiral_restr0.0790.274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02581
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02112
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_it3.93.846267
X-RAY DIFFRACTIONr_mcbond_other3.9073.839266
X-RAY DIFFRACTIONr_mcangle_it4.4195.745332
X-RAY DIFFRACTIONr_mcangle_other4.4165.751333
X-RAY DIFFRACTIONr_scbond_it4.9334.478272
X-RAY DIFFRACTIONr_scbond_other4.8384.472270
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9246.48389
X-RAY DIFFRACTIONr_long_range_B_refined7.89845.327584
X-RAY DIFFRACTIONr_long_range_B_other7.88745.258582
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_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 %

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