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- PDB-5yi2: Structure of Lactococcus lactis ZitR, wild type in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 5yi2
TitleStructure of Lactococcus lactis ZitR, wild type 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 / Zinc binding protein / MarR family / winged Helix-turn-helix / Transcriptional regulator
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: 2.6 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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')
D: 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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,78232
Polymers170,73616
Non-polymers1,04716
Water6,882382
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)42,9468
Polymers42,6844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8760 Å2
ΔGint-159 kcal/mol
Surface area20220 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)42,9468
Polymers42,6844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-159 kcal/mol
Surface area20240 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)42,9468
Polymers42,6844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-157 kcal/mol
Surface area20420 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)42,9468
Polymers42,6844
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8720 Å2
ΔGint-158 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.616, 101.568, 101.544
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Zinc transport transcriptional regulator


Mass: 16445.750 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (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.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.62 Å3/Da / Density % sol: 52.97 %
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: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 64593 / % possible obs: 98.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.9
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.984 / Mean I/σ(I) obs: 2 / Num. unique obs: 1463 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DMT, 3Q5F

5dmt
PDB Unreleased entry

3q5f


Resolution: 2.6→40.116 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1620 3.11 %
Rwork0.1912 --
obs0.193 52172 96.26 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.175 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4086 Å2-0 Å2-9.7081 Å2
2--0.4139 Å20 Å2
3---2.9947 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9190 2600 16 382 12188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812214
X-RAY DIFFRACTIONf_angle_d1.24416999
X-RAY DIFFRACTIONf_dihedral_angle_d21.3924775
X-RAY DIFFRACTIONf_chiral_restr0.072008
X-RAY DIFFRACTIONf_plane_restr0.0041705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.36161510.25994887X-RAY DIFFRACTION94
2.6929-2.80070.35021670.25064937X-RAY DIFFRACTION95
2.8007-2.92810.34791580.25594984X-RAY DIFFRACTION95
2.9281-3.08250.30331510.24715022X-RAY DIFFRACTION96
3.0825-3.27550.32161670.21955077X-RAY DIFFRACTION97
3.2755-3.52830.24771620.2145071X-RAY DIFFRACTION97
3.5283-3.88310.28761670.18825138X-RAY DIFFRACTION98
3.8831-4.44430.21781670.16375124X-RAY DIFFRACTION98
4.4443-5.5970.20591710.1675160X-RAY DIFFRACTION98
5.597-40.12070.15981590.14755152X-RAY DIFFRACTION96

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