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- PDB-5yi3: Structure of Lactococcus lactis ZitR, C30S mutant in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5yi3
TitleStructure of Lactococcus lactis ZitR, C30S mutant in complex with DNA
Components
  • DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
  • Zinc transport transcriptional regulator
KeywordsMETAL BINDING PROTEIN/DNA / Zinc binding protein / MarR family / winged Helix-turn-helix / Transcriptional regulator / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / zinc ion binding
Similarity search - Function
Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / : / : / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins ...Helix Hairpins - #1680 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2360 / : / : / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Special / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc transport transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
Lactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSong, Y. / Liu, H. / Zhu, R. / Yi, C. / Chen, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Basic Research Foundation of China2010CB912302 2012CB917301 China
National Natural Science Foundation of China21225206 91013005 21001010 China
E-Institutes of Shanghai Municipal Education CommissionE09013 China
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2017
Title: Allosteric histidine switch for regulation of intracellular zinc(II) fluctuation.
Authors: Zhu, R. / Song, Y. / Liu, H. / Yang, Y. / Wang, S. / Yi, C. / Chen, P.R.
History
DepositionOct 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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: Zinc transport transcriptional regulator
B: Zinc transport transcriptional regulator
C: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
E: Zinc transport transcriptional regulator
F: Zinc transport transcriptional regulator
G: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
I: Zinc transport transcriptional regulator
J: Zinc transport transcriptional regulator
K: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
M: Zinc transport transcriptional regulator
N: Zinc transport transcriptional regulator
O: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
P: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
L: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
H: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,13024
Polymers170,60716
Non-polymers5238
Water46826
1
A: Zinc transport transcriptional regulator
B: Zinc transport transcriptional regulator
C: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
D: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7836
Polymers42,6524
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-83 kcal/mol
Surface area20350 Å2
MethodPISA
2
E: Zinc transport transcriptional regulator
F: Zinc transport transcriptional regulator
G: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
H: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7836
Polymers42,6524
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-87 kcal/mol
Surface area20070 Å2
MethodPISA
3
I: Zinc transport transcriptional regulator
J: Zinc transport transcriptional regulator
K: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
L: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7836
Polymers42,6524
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-82 kcal/mol
Surface area19860 Å2
MethodPISA
4
M: Zinc transport transcriptional regulator
N: Zinc transport transcriptional regulator
O: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
P: DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7836
Polymers42,6524
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8260 Å2
ΔGint-81 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.522, 103.058, 104.855
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Zinc transport transcriptional regulator


Mass: 16429.686 Da / Num. of mol.: 8 / Mutation: C30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria)
Strain: IL1403 / Gene: zitR, L168265 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9CDU5
#2: DNA chain
DNA (5'-D(*TP*GP*TP*TP*AP*AP*CP*TP*AP*GP*TP*TP*AP*AP*CP*A)-3')


Mass: 4896.215 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Sodium cacodylate pH 6.1, 0.05M Magnesium chloride hexahydrate, 0.1M Sodium chloride, 20%(w/v) Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 18, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 47584 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4718 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q5F

3q5f


Resolution: 2.9→42.486 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1659 4.33 %
Rwork0.2053 --
obs0.2078 38357 90.73 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.994 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.2611 Å2-0 Å2-42.337 Å2
2---20.7739 Å20 Å2
3---27.035 Å2
Refinement stepCycle: LAST / Resolution: 2.9→42.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9083 2600 8 26 11717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912107
X-RAY DIFFRACTIONf_angle_d1.32816869
X-RAY DIFFRACTIONf_dihedral_angle_d21.5374701
X-RAY DIFFRACTIONf_chiral_restr0.0691999
X-RAY DIFFRACTIONf_plane_restr0.0041691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.4411470.34433100X-RAY DIFFRACTION77
3.0037-3.12390.40911370.31423148X-RAY DIFFRACTION78
3.1239-3.2660.31431570.25273386X-RAY DIFFRACTION84
3.266-3.43820.32961660.23593649X-RAY DIFFRACTION91
3.4382-3.65350.27841760.22713825X-RAY DIFFRACTION95
3.6535-3.93540.31051590.2213827X-RAY DIFFRACTION95
3.9354-4.33110.25951850.18623894X-RAY DIFFRACTION96
4.3311-4.95690.2191690.17543960X-RAY DIFFRACTION97
4.9569-6.24210.26191770.20793994X-RAY DIFFRACTION98
6.2421-42.49070.19241860.15653915X-RAY DIFFRACTION95

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