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- PDB-5za3: Structure of a C-terminal S. mutans response regulator VicR domain -

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Basic information

Entry
Database: PDB / ID: 5za3
TitleStructure of a C-terminal S. mutans response regulator VicR domain
ComponentsDNA-binding response regulator
KeywordsSIGNALING PROTEIN / dimer / two component system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
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/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-binding response regulator
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCai, Y.F. / Hu, X.J. / San, J.Y. / Han, A.D.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structure of a C-terminal S. mutans response regulator VicR domain
Authors: Cai, Y.F. / Hu, X.J. / San, J.Y. / Han, A.D.
History
DepositionFeb 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / Item: _citation.unpublished_flag
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)23,8172
Polymers23,8172
Non-polymers00
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint1 kcal/mol
Surface area11420 Å2
Unit cell
Length a, b, c (Å)39.647, 83.984, 39.978
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA-binding response regulator / Responder protein CovR


Mass: 11908.535 Da / Num. of mol.: 2 / Fragment: C terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: covR, A6J86_03970 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q93MY4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 9
Details: 100 mM BICINE, pH 9.0, 20% polyethylene glycerol 6000

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Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. obs: 35819 / % possible obs: 90 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.0649 / Rsym value: 0.0649 / Net I/σ(I): 35.388
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000v706data reduction
HKL-2000v706data scaling
PHENIX1.8.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZXJ

2zxj


Resolution: 1.5→20.442 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 20.99
RfactorNum. reflection% reflection
Rfree0.2216 1782 4.98 %
Rwork0.1975 --
obs0.1987 35793 89.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→20.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 0 314 1984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051708
X-RAY DIFFRACTIONf_angle_d1.0192311
X-RAY DIFFRACTIONf_dihedral_angle_d11.964643
X-RAY DIFFRACTIONf_chiral_restr0.037257
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4971-1.53750.2561450.2742792X-RAY DIFFRACTION95
1.5375-1.58280.28981520.2532896X-RAY DIFFRACTION99
1.5828-1.63380.27281480.23752879X-RAY DIFFRACTION99
1.6338-1.69220.25211530.23032877X-RAY DIFFRACTION99
1.6922-1.75990.21621530.22292869X-RAY DIFFRACTION98
1.7599-1.840.21721560.21742866X-RAY DIFFRACTION99
1.84-1.93690.311450.2172823X-RAY DIFFRACTION96
1.9369-2.05820.23131520.19892823X-RAY DIFFRACTION97
2.0582-2.21690.21481510.18462838X-RAY DIFFRACTION96
2.2169-2.43970.19771360.18132655X-RAY DIFFRACTION91
2.4397-2.79190.19021330.18212610X-RAY DIFFRACTION89
2.7919-3.51460.21121130.18142212X-RAY DIFFRACTION75
3.5146-20.44390.2411450.2186871X-RAY DIFFRACTION29
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)
16.8757-4.0319-0.64162.57681.19674.97980.10060.0158-0.62450.1431-0.26430.53980.2619-0.29640.15180.2755-0.0357-0.02790.21980.02670.3358-5.4202-18.4378-13.4165
23.06060.2263-0.274.5839-1.17262.33350.16460.1152-0.10090.04490.03720.23560.05-0.0541-0.1240.1784-0.0205-0.00830.2295-0.00190.22761.0651-13.2903-16.9888
32.7042-1.25391.45164.2455-2.37876.40670.01840.14290.0983-0.0388-0.0324-0.1369-0.28440.0777-0.02030.1889-0.03060.0060.28450.01110.20418.0826-5.4076-20.3716
47.23540.9840.59725.58210.91146.9520.1875-0.2872-0.57050.3791-0.0904-0.45370.65510.1688-0.01780.24590.0234-0.03540.18150.01990.31211.4114-19.9113-16.0148
55.0928-1.6096-1.17372.45743.8036.42140.27240.32930.3588-0.1003-0.1809-0.3064-0.46870.0564-0.09620.36740.0170.06510.24680.04440.3056-4.905311.1011-14.9068
63.38652.08260.4718.74932.05173.71790.1095-0.10450.0181-0.0757-0.2261-0.2555-0.47930.434-0.01040.2541-0.04470.04260.2469-0.0110.30120.86285.6067-10.4472
72.93051.0059-0.60823.85940.2483.6045-0.12730.20910.2449-0.1824-00.2521-0.1686-0.54890.05040.2208-0.0034-0.01220.31790.0020.1901-13.83244.3132-9.4136
84.63252.20572.70513.5642.01772.59520.1416-0.2397-0.16930.1538-0.11380.14110.1861-0.3552-0.06780.2012-0.04040.01950.36080.02440.196-14.7165-3.2964-3.6275
95.6826-0.10811.17575.54960.14119.1257-0.0797-0.10780.66420.1988-0.04280.0862-0.9294-0.56890.13970.3760.04120.00730.2585-0.05370.2583-11.612710.60671.2943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 135 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 180 )
3X-RAY DIFFRACTION3chain 'A' and (resid 181 through 211 )
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 235 )
5X-RAY DIFFRACTION5chain 'B' and (resid 135 through 148 )
6X-RAY DIFFRACTION6chain 'B' and (resid 149 through 161 )
7X-RAY DIFFRACTION7chain 'B' and (resid 162 through 180 )
8X-RAY DIFFRACTION8chain 'B' and (resid 181 through 211 )
9X-RAY DIFFRACTION9chain 'B' and (resid 212 through 234 )

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