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- PDB-7ve4: C-terminal domain of VraR -

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Basic information

Entry
Database: PDB / ID: 7ve4
TitleC-terminal domain of VraR
ComponentsDNA-binding response regulator
KeywordsDNA BINDING PROTEIN / two-component system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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
DNA-binding response regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsKumar, J.V. / Chen, C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)110-2628-B-002 -049 Taiwan
Ministry of Science and Technology (MoST, Taiwan)110-2113-M-002 -023 Taiwan
CitationJournal: Protein Sci. / Year: 2022
Title: Structural insights into DNA binding domain of vancomycin-resistance-associated response regulator in complex with its promoter DNA from Staphylococcus aureus.
Authors: Kumar, J.V. / Tseng, T.S. / Lou, Y.C. / Wei, S.Y. / Wu, T.H. / Tang, H.C. / Chiu, Y.C. / Hsu, C.H. / Chen, C.
History
DepositionSep 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)8,3431
Polymers8,3431
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4410 Å2
Unit cell
Length a, b, c (Å)50.963, 50.963, 81.063
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein DNA-binding response regulator


Mass: 8342.708 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: BSZ10_05280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q8DEZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 3.38 Å3/Da / Density % sol: 69.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris-Hcl pH 8.5, 16% PEG 4000 (w/v), 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jan 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.87→24.31 Å / Num. obs: 9739 / % possible obs: 98.4 % / Redundancy: 5.7 % / Biso Wilson estimate: 27.25 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 29.88
Reflection shellResolution: 1.87→1.93 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.51 / Num. unique obs: 842

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IF4

4if4


Resolution: 1.87→24.309 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 966 9.92 %
Rwork0.162 8776 -
obs0.1645 9738 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.99 Å2 / Biso mean: 25.2262 Å2 / Biso min: 7.71 Å2
Refinement stepCycle: final / Resolution: 1.87→24.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms547 0 0 121 668
Biso mean---37.42 -
Num. residues----68
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.87-1.96840.2441290.2187114690
1.9684-2.09170.21381360.17781254100
2.0917-2.25310.17531460.1591263100
2.2531-2.47960.21561350.16241267100
2.4796-2.8380.16831410.1531287100
2.838-3.57370.18961350.16661275100
3.5737-24.3090.1691440.1491128499
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)
14.0421-0.4822-2.24881.8332-0.09351.8634-0.10130.16780.0591-0.2071-0.22490.33510.015-0.60920.24570.15910.0067-0.05990.3505-0.13090.200419.1093-11.0194-4.1029
23.7886-0.2379-0.39413.65730.34764.83180.0859-0.07150.01150.1354-0.13670.08020.0101-0.20880.03870.0733-0.0401-0.00770.108-0.01610.095122.4146-4.0297.5205
33.60280.4317-0.61131.3327-0.2980.4902-0.04070.0663-0.09770.0079-0.02810.16090.0729-0.09820.08690.2585-0.18980.07030.3207-0.08850.293915.1538-14.1918.6663
42.44953.08060.11845.6870.07666.49040.08710.0193-0.72490.0961-0.1333-0.32670.72620.00320.03360.15140.0054-0.00280.1252-0.04380.200726.3266-13.56413.4856
51.71671.6690.24085.93063.85075.15310.0989-0.1581-0.09150.19690.1035-0.35720.24970.3389-0.18120.24240.03370.03510.1912-0.0390.167433.0349-13.2217-5.0123
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 176 through 194 )A176 - 194
2X-RAY DIFFRACTION2chain 'A' and (resid 195 through 209 )A195 - 209
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 149 )A142 - 149
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 161 )A150 - 161
5X-RAY DIFFRACTION5chain 'A' and (resid 162 through 175 )A162 - 175

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