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- PDB-7e92: Crystal structure of the DNA-binding domain of the response regul... -

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Basic information

Entry
Database: PDB / ID: 7.0E+92
TitleCrystal structure of the DNA-binding domain of the response regulator VbrR from Vibrio parahaemolyticus
ComponentsDNA-binding response regulator
KeywordsTRANSCRIPTION / transcriptional regulation / DNA-binding domain / response regulator / VbrR / Vibrio parahaemolyticus
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / 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 / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus.
Authors: Cho, S.Y. / Yoon, S.I.
History
DepositionMar 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Data collection / Category: diffrn_radiation / Item: _diffrn_radiation.wavelength_id
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)24,3262
Polymers24,3262
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-35 kcal/mol
Surface area10380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.315, 51.758, 97.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA-binding response regulator / Response regulator / Response regulator transcription factor / Transcriptional regulator


Mass: 12162.881 Da / Num. of mol.: 2 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria)
Gene: ACS84_09205, C9I78_18460, CA163_10520, CGH73_12770, D5E78_24805, F0L89_03250, F0L99_22745, WR32_19050
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L8SKF9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.83 Å3/Da / Density % sol: 32.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400, MES, PEG 3350

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.9793
SYNCHROTRONPAL/PLS 11C20.9794, 0.9796, 0.9717
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDNov 2, 2019
DECTRIS PILATUS 6M2PIXELJul 1, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.97961
40.97171
ReflectionResolution: 1.8→30 Å / Num. obs: 17222 / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 33.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 838 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 844 4.93 %
Rwork0.186 --
obs0.1882 16280 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 83 1601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051544
X-RAY DIFFRACTIONf_angle_d0.7282090
X-RAY DIFFRACTIONf_dihedral_angle_d17.187921
X-RAY DIFFRACTIONf_chiral_restr0.049250
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.91280.26381280.23022669X-RAY DIFFRACTION100
1.9128-2.06050.28491360.21242684X-RAY DIFFRACTION100
2.0605-2.26770.28311330.19392672X-RAY DIFFRACTION100
2.2677-2.59570.24841480.20182692X-RAY DIFFRACTION100
2.5957-3.26960.24981500.20662726X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.8356-2.03652.71494.7071-0.76556.48550.70860.0925-0.7497-1.0453-0.11120.64340.70680.0792-0.48190.44320.0412-0.06020.26780.01930.35197.6354-2.8763-33.8326
24.2557-0.56220.08325.9553-3.61952.275-0.0304-0.2293-0.3415-0.00570.0895-0.0899-0.1437-0.40780.03260.37810.05960.01070.225-0.02470.259913.7584-3.1934-30.0431
34.64-1.63770.00214.68630.48885.7423-0.1209-0.1592-0.1901-0.13860.0839-0.08360.2701-0.10350.0190.20060.01290.00460.11720.00030.138.82694.1834-26.6608
45.77460.9270.673.9828-5.12677.2838-0.2502-0.1884-0.2032-0.40860.19850.00470.3698-0.72050.02620.25960.00460.04210.2566-0.02090.18435.78.5842-15.6854
58.74646.73066.42935.39375.64416.93210.1548-0.1261-0.5540.4829-0.0937-0.45541.02340.3818-0.04510.28660.0360.02570.23370.0050.28358.20846.815-6.8648
64.3078-0.9913-2.2056.96944.89074.0670.15020.1764-0.2020.29830.0385-0.09270.3519-0.4901-0.22190.1650.0072-0.01460.18540.02560.20873.252717.3273.6873
72.99863.3364-2.06024.3196-1.33036.6605-0.20940.18850.3733-0.2718-0.09950.5692-1.0153-0.76830.25280.32430.1552-0.04560.37240.00250.29190.329827.60392.36
89.1418-5.04720.07742.91260.25614.59710.0162-0.04940.45650.3134-0.0851-0.4559-0.30850.2740.06040.35060.0251-0.0440.20420.01670.280412.049232.99511.8679
95.8701-2.364-0.86285.5872-0.4162.6102-0.18470.32780.33670.6212-0.0962-0.330.09540.33120.2930.32560.0117-0.04390.26630.00770.192315.160425.924813.7746
102.804-0.830.18286.25780.01442.3982-0.0310.0122-0.10510.4805-0.0432-0.0302-0.3150.17050.04620.21950.0078-0.02840.1785-0.03840.153211.258823.40859.2417
116.02613.87345.29182.6463.4494.6559-0.23070.42290.2778-1.09790.0087-0.2189-1.30650.19250.38970.48930.0629-0.01310.24120.03010.25947.306231.493-3.1199
126.156-2.71560.49815.93131.28252.17950.0848-0.16640.5353-0.34240.047-0.3454-0.5020.1005-0.10080.2118-0.02990.03210.2607-0.00540.187710.340220.775-5.6048
136.74653.81495.5023.3324.7476.76160.1310.5243-0.112-0.45450.0805-0.8479-0.69710.6845-0.20060.237-0.04760.0290.2243-0.00780.248616.552415.483-9.282
146.9541-3.3535-4.86725.51223.91574.1899-0.00440.04490.0697-0.3431-0.1354-0.3052-0.45270.39430.07180.1705-0.00850.00150.15510.0240.2212.809113.89-23.9532
153.6171-4.4069-5.73269.00686.199.4669-0.06250.1317-0.0408-0.2723-0.16750.5894-0.7565-0.40060.25890.43040.074-0.01620.243-0.01110.22684.510514.7189-29.8761
164.09973.45282.50342.92292.00022.0511-0.093-0.03840.3838-0.23680.2131-0.2692-0.2636-0.3497-0.04090.33790.0905-0.01250.29240.02740.26631.66511.4485-27.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 145 )
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 172 )
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 188 )
6X-RAY DIFFRACTION6chain 'A' and (resid 189 through 202 )
7X-RAY DIFFRACTION7chain 'A' and (resid 203 through 220 )
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 137 )
9X-RAY DIFFRACTION9chain 'B' and (resid 138 through 145 )
10X-RAY DIFFRACTION10chain 'B' and (resid 146 through 164 )
11X-RAY DIFFRACTION11chain 'B' and (resid 165 through 172 )
12X-RAY DIFFRACTION12chain 'B' and (resid 173 through 181 )
13X-RAY DIFFRACTION13chain 'B' and (resid 182 through 188 )
14X-RAY DIFFRACTION14chain 'B' and (resid 189 through 202 )
15X-RAY DIFFRACTION15chain 'B' and (resid 203 through 214 )
16X-RAY DIFFRACTION16chain 'B' and (resid 215 through 219 )

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