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- PDB-7ve6: N-terminal domain of VraR -

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Basic information

Entry
Database: PDB / ID: 7ve6
TitleN-terminal domain of VraR
ComponentsResponse regulator protein VraR
KeywordsDNA BINDING PROTEIN / two-component system
Function / homology
Function and homology information


phosphorelay signal transduction system / response to antibiotic / regulation of DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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. ...LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / 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 / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Response regulator protein VraR
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 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: Response regulator protein VraR
B: Response regulator protein VraR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3636
Polymers47,1832
Non-polymers1814
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-29 kcal/mol
Surface area12000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.713, 122.713, 67.522
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 2 - 137 / Label seq-ID: 2 - 137

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

NCS oper: (Code: givenMatrix: (0.614316305434, 0.497461112397, -0.612493198763), (0.49016433004, -0.848882677402, -0.197831063191), (-0.618348127218, -0.178691470586, -0.765320163008)Vector: -40. ...NCS oper: (Code: given
Matrix: (0.614316305434, 0.497461112397, -0.612493198763), (0.49016433004, -0.848882677402, -0.197831063191), (-0.618348127218, -0.178691470586, -0.765320163008)
Vector: -40.042353371, 65.2078269064, -52.4300957543)

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Components

#1: Protein Response regulator protein VraR


Mass: 23591.340 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain Mu50 / ATCC 700699) (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: vraR, SAV1884 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7A2Q1
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-Hcl pH 8.0, 18% PEG 550MME (w/v), 5% Glycerol, 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: 0.9984 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9984 Å / Relative weight: 1
ReflectionResolution: 2.77→22.93 Å / Num. obs: 14756 / % possible obs: 97.24 % / Redundancy: 9.2 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 37.16
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.142 / Num. unique obs: 1152

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Processing

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

4if4


Resolution: 2.77→22.93 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 2311 10.02 %
Rwork0.178 20756 -
obs-14754 79.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.62 Å2 / Biso mean: 46.2841 Å2 / Biso min: 17.65 Å2
Refinement stepCycle: final / Resolution: 2.77→22.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 10 24 2146
Biso mean--30.65 33.28 -
Num. residues----272
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A822X-RAY DIFFRACTION4.446TORSIONAL
12B822X-RAY DIFFRACTION4.446TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.77-2.830.3933550.306853035
2.83-2.890.3106830.298375449
2.89-2.960.2898850.256579152
2.96-3.030.3338900.25580852
3.03-3.110.2799880.270383254
3.11-3.20.29481150.254790560
3.2-3.310.33911160.1994110873
3.31-3.420.29231580.1871137890
3.42-3.560.27161670.1998150499
3.56-3.720.24391750.18361547100
3.72-3.920.20551700.15911498100
3.92-4.160.20551650.15411527100
4.17-4.480.17171580.13181540100
4.48-4.930.15851640.13031533100
4.93-5.630.20571760.16391528100
5.63-7.050.26641700.19951519100
7.07-22.930.18751760.1731145496

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