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- PDB-5yi1: Structure of Lactococcus lactis ZitR, C30AH42A mutant in apo form -

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Basic information

Entry
Database: PDB / ID: 5yi1
TitleStructure of Lactococcus lactis ZitR, C30AH42A mutant in apo form
ComponentsZinc 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
: / : / MarR family / ArsR-like helix-turn-helix domain / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Zinc transport transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Assembly

Deposited unit
A: Zinc transport transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)16,3471
Polymers16,3471
Non-polymers00
Water37821
1
A: Zinc transport transcriptional regulator

A: Zinc transport transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)32,6932
Polymers32,6932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area3790 Å2
ΔGint-44 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.115, 61.115, 123.653
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Zinc transport transcriptional regulator


Mass: 16346.614 Da / Num. of mol.: 1 / Mutation: C30A, H42A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.51 Å3/Da / Density % sol: 64.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 63%(v/v) Polyethylene glycol 200, 10mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 14987 / % possible obs: 98.7 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 30.9
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1463 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.6.2_432refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YI0

5yi0


Resolution: 2.2→27.585 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 625 5.17 %
Rwork0.2583 --
obs0.2588 12078 96.38 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.896 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4692 Å2-0 Å20 Å2
2---6.4692 Å20 Å2
3---12.9384 Å2
Refinement stepCycle: LAST / Resolution: 2.2→27.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 0 0 21 1058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081048
X-RAY DIFFRACTIONf_angle_d0.9031411
X-RAY DIFFRACTIONf_dihedral_angle_d16.528394
X-RAY DIFFRACTIONf_chiral_restr0.056171
X-RAY DIFFRACTIONf_plane_restr0.004178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.42130.33821450.25712759X-RAY DIFFRACTION95
2.4213-2.77140.30461670.25592815X-RAY DIFFRACTION97
2.7714-3.49060.30221540.26122921X-RAY DIFFRACTION99
3.4906-27.58730.24231590.25772958X-RAY DIFFRACTION95

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