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- PDB-7ve5: C-terminal domain of VraR -

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Basic information

Entry
Database: PDB / ID: 7ve5
TitleC-terminal domain of VraR
Components
  • (R1-DNA) x 2
  • DNA-binding response regulator
KeywordsDNA BINDING PROTEIN/DNA / two-component system / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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 / DNA (> 10) / DNA-binding response regulator
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding response regulator
B: DNA-binding response regulator
C: R1-DNA
D: R1-DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,33010
Polymers30,1844
Non-polymers1466
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-83 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.349, 60.349, 171.521
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 143 - 208 / Label seq-ID: 6 - 71

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein DNA-binding response regulator


Mass: 8342.708 Da / Num. of mol.: 2
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: DNA chain R1-DNA


Mass: 6767.430 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
#3: DNA chain R1-DNA


Mass: 6731.374 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 100 mM Sodium cacodylate pH 6.6, 10% PEG 1500 (w/v), 5% PEG 400 (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: Dec 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.99→22.31 Å / Num. obs: 14143 / % possible obs: 89.21 % / Redundancy: 2 % / Biso Wilson estimate: 22.05 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.29
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.402 / Num. unique obs: 1129

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IF4

4if4


Resolution: 2→22.31 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 27.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2549 1403 9.92 %
Rwork0.1945 12736 -
obs0.2005 14139 89.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.07 Å2 / Biso mean: 23.1727 Å2 / Biso min: 10.05 Å2
Refinement stepCycle: final / Resolution: 2→22.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 779 6 135 1984
Biso mean--23.84 24.45 -
Num. residues----170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A394X-RAY DIFFRACTION0.887TORSIONAL
12B394X-RAY DIFFRACTION0.887TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.070.30461060.21051023112971
2.07-2.150.30051270.19661139126680
2.15-2.250.30061360.19451217135386
2.25-2.370.28781340.2091281141590
2.37-2.510.30331500.20831323147393
2.51-2.710.30011500.22341358150895
2.71-2.980.27751470.21181352149996
2.98-3.410.25251490.19311344149394
3.41-4.290.22881520.17131326147893
4.29-22.310.20161520.18621373152596

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