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- PDB-7vim: The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida -

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Basic information

Entry
Database: PDB / ID: 7vim
TitleThe C-terminal DNA binding domain of EsrB from Edwardsiella piscicida
ComponentsProtein EsrB
KeywordsDNA BINDING PROTEIN / DNA binding / EsrB / Edwardsiella piscicida
Function / homology
Function and homology information


phosphorelay signal transduction system / 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 / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily
Similarity search - Domain/homology
Biological speciesEdwardsiella piscicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.2 Å
AuthorsLiu, B. / Reverter, D. / Shao, S.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2015-66417-P (MINECO/FEDER) Spain
CitationJournal: To Be Published
Title: The C-terminal DNA binding domain of EsrB from Edwardsiella piscicida
Authors: Liu, B. / Reverter, D. / Shao, S.
History
DepositionSep 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein EsrB
B: Protein EsrB


Theoretical massNumber of molelcules
Total (without water)16,5572
Polymers16,5572
Non-polymers00
Water37821
1
A: Protein EsrB

B: Protein EsrB


Theoretical massNumber of molelcules
Total (without water)16,5572
Polymers16,5572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area780 Å2
ΔGint-9 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.111, 58.051, 81.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein EsrB / Two component system response regulator


Mass: 8278.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Edwardsiella piscicida (bacteria) / Gene: EVK84_02890, MA13_contig00007-0127 / Plasmid: pET28 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A034T5T1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 12% ethanol, 5% glycerol, 100mM Tris PH 8,5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.188→47.193 Å / Num. obs: 9987 / % possible obs: 99.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 41.97 Å2 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Rsym value: 0.076 / Net I/av σ(I): 5.7 / Net I/σ(I): 11.4 / Num. measured all: 62270
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.19-2.316.10.6431.1829413680.2780.7020.643396.1
2.31-2.456.20.4481.5849713610.1970.490.4484.4100
2.45-2.616.50.2682.4836412830.1150.2920.2686100
2.61-2.826.20.173.9738211850.0740.1850.177.2100
2.82-3.096.40.1056.4710611030.0450.1140.10510.3100
3.09-3.466.40.0798.3646410150.0340.0860.07913.6100
3.46-3.996.20.0649.555869000.0280.070.06420.5100
3.99-4.896.20.05211.648237840.0230.0570.05225.1100
4.89-6.926.10.05311.237016090.0240.0580.05321.8100
6.92-47.1935.40.04310.420533790.020.0470.04328.699.8

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.2→47.193 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 473 4.81 %
Rwork0.2293 9368 -
obs0.2316 9841 99.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.085 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 43.39 Å2 / Biso min: 20.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.8692 Å2-0 Å20 Å2
2---1.0262 Å20 Å2
3---3.6888 Å2
Refinement stepCycle: final / Resolution: 2.2→47.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 0 21 1077
Biso mean---41.07 -
Num. residues----131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081066
X-RAY DIFFRACTIONf_angle_d1.1121433
X-RAY DIFFRACTIONf_chiral_restr0.067171
X-RAY DIFFRACTIONf_plane_restr0.003182
X-RAY DIFFRACTIONf_dihedral_angle_d14.303425
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.2-2.51840.38571570.28283040
2.5184-3.17280.2881520.22513095
3.1728-47.1930.25651640.22073233

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