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- PDB-5cvi: Structure of the manganese regulator SloR -

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Basic information

Entry
Database: PDB / ID: 5cvi
TitleStructure of the manganese regulator SloR
ComponentsSloR
KeywordsTranscription regulator / manganese regulator / DtxR family
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain ...FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Manganese transport regulator
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsNye, D. / Glasfeld, A.
CitationJournal: to be published
Title: SloR structure and DNA binding studies inform the SloR-SRE interaction in Streptococcus mutans
Authors: Spatafora, G. / Corbett, J. / Cornacchione, L.P. / Daly, W.C. / Galan-Donlo, D. / Wysota, M. / Tivnan, P. / Collins, J. / Nye, D. / Levitz, T. / Breyer, W.A. / Glasfeld, A.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 26, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SloR
B: SloR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90511
Polymers50,3202
Non-polymers5859
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-219 kcal/mol
Surface area22440 Å2
MethodPISA
2
A: SloR
hetero molecules

B: SloR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,90511
Polymers50,3202
Non-polymers5859
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area1090 Å2
ΔGint-229 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.432, 60.432, 298.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SloR


Mass: 25160.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: sloR / Plasmid: pSMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9KIJ2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 3350, 40 mM lithium sulfate, 1 mM zinc chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9785 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.8→59.23 Å / Num. obs: 25853 / % possible obs: 99.7 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 25
Reflection shellResolution: 2.8→2.96 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 5.1 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→59.23 Å / FOM work R set: 0.8545 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1307 5.06 %
Rwork0.1997 24546 -
obs0.2025 25853 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.9 Å2 / Biso mean: 35.99 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 2.804→59.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 18 32 3520
Biso mean--27.92 21.9 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033539
X-RAY DIFFRACTIONf_angle_d0.5654766
X-RAY DIFFRACTIONf_chiral_restr0.044539
X-RAY DIFFRACTIONf_plane_restr0.001604
X-RAY DIFFRACTIONf_dihedral_angle_d13.3231366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8037-2.9160.34191630.26212632279597
2.916-3.04870.30751570.234527522909100
3.0487-3.20940.28931340.224927422876100
3.2094-3.41050.28241230.219827542877100
3.4105-3.67380.29841540.209727102864100
3.6738-4.04340.24021550.184527432898100
4.0434-4.62830.23081340.174427382872100
4.6283-5.83040.26091650.182927042869100
5.8304-59.24570.20241220.197327712893100
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)
12.60021.6399-0.21272.83780.84232.38190.2839-0.57550.58390.0675-0.26060.2406-0.7061-0.0640.02820.3606-0.04480.0690.3853-0.13250.344829.8471-0.6571124.8745
20.0978-0.3144-0.27681.10910.44193.56070.1817-0.1969-0.05430.3302-0.0288-0.0522-0.13470.0938-0.11360.1952-0.0775-0.05970.2256-0.0350.152650.3958-4.2181125.361
35.7866-0.06421.88482.32360.7981.80340.36030.1172-0.2233-0.0419-0.1411-0.11110.1343-0.1473-0.18960.32270.0027-0.02020.23080.06010.207435.85016.994483.8039
40.8370.50480.30481.75652.21284.37160.03390.0813-0.0109-0.33150.0825-0.0887-0.27940.1204-0.15140.1748-0.016-0.00910.1220.01170.166250.6211-7.574282.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:67)A3 - 67
2X-RAY DIFFRACTION2(chain A and resid 68:214)A68 - 214
3X-RAY DIFFRACTION3(chain B and resid 1:70)B1 - 70
4X-RAY DIFFRACTION4(chain B and resid 71:215)B71 - 215

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