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- PDB-5yi0: Structure of Lactococcus lactis ZitR, C30AH42A mutant -

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Basic information

Entry
Database: PDB / ID: 5yi0
TitleStructure of Lactococcus lactis ZitR, C30AH42A mutant
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
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
Zinc transport transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: Zinc transport transcriptional regulator
A: Zinc transport transcriptional regulator
C: Zinc transport transcriptional regulator
D: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6488
Polymers65,3864
Non-polymers2624
Water1,72996
1
B: Zinc transport transcriptional regulator
hetero molecules

B: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8244
Polymers32,6932
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4170 Å2
ΔGint-48 kcal/mol
Surface area17890 Å2
MethodPISA
2
A: Zinc transport transcriptional regulator
C: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8244
Polymers32,6932
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-48 kcal/mol
Surface area17790 Å2
MethodPISA
3
D: Zinc transport transcriptional regulator
hetero molecules

D: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8244
Polymers32,6932
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4200 Å2
ΔGint-49 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.038, 86.864, 126.783
Angle α, β, γ (deg.)90.00, 90.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Zinc transport transcriptional regulator


Mass: 16346.614 Da / Num. of mol.: 4 / 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: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.66 Å3/Da / Density % sol: 66.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 42%(v/v) Polyethylene glycol 200

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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: Nov 23, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 49739 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.3
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2585 / % possible all: 99.1

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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: 5YHY

5yhy


Resolution: 2.3→19.549 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3008 1605 4.04 %
Rwork0.2513 --
obs0.2533 39696 94.48 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.949 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.8442 Å20 Å23.2871 Å2
2---2.4113 Å2-0 Å2
3----3.433 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 4 96 4684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084636
X-RAY DIFFRACTIONf_angle_d1.0836240
X-RAY DIFFRACTIONf_dihedral_angle_d16.7091756
X-RAY DIFFRACTIONf_chiral_restr0.071752
X-RAY DIFFRACTIONf_plane_restr0.004788
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38210.29841530.27663645X-RAY DIFFRACTION91
2.3821-2.47730.36541550.26913756X-RAY DIFFRACTION93
2.4773-2.58980.32621590.27383767X-RAY DIFFRACTION94
2.5898-2.7260.27191650.26083836X-RAY DIFFRACTION96
2.726-2.89630.29911600.2723886X-RAY DIFFRACTION96
2.8963-3.1190.2921590.27313957X-RAY DIFFRACTION98
3.119-3.43140.34671720.28473959X-RAY DIFFRACTION98
3.4314-3.92440.3121620.24213864X-RAY DIFFRACTION96
3.9244-4.93120.26641560.23053711X-RAY DIFFRACTION92
4.9312-19.54930.29081640.23843710X-RAY DIFFRACTION90

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