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- PDB-5yhz: Structure of Lactococcus lactis ZitR, E41A mutant -

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Basic information

Entry
Database: PDB / ID: 5yhz
TitleStructure of Lactococcus lactis ZitR, E41A 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
DI(HYDROXYETHYL)ETHER / Zinc transport transcriptional regulator
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Assembly

Deposited unit
A: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8205
Polymers16,3881
Non-polymers4324
Water1,31573
1
A: Zinc transport transcriptional regulator
hetero molecules

A: Zinc transport transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,64010
Polymers32,7752
Non-polymers8648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4110 Å2
ΔGint-47 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.357, 94.238, 31.915
Angle α, β, γ (deg.)90.00, 110.10, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-367-

HOH

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Components

#1: Protein Zinc transport transcriptional regulator


Mass: 16387.715 Da / Num. of mol.: 1 / Mutation: E41A
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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 3.33 Å3/Da / Density % sol: 63.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.05M Calcium chloride dihydrate, 0.1M MES monohydrate pH 6.0, 45%(v/v) Polyethylene glycol 200

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9795 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 17200 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.9
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1711 / % 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: 5YHX

5yhx


Resolution: 1.9→30.156 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1586 9.97 %
Rwork0.2195 --
obs0.223 15905 93.88 %
Solvent computationShrinkage radii: 1.13 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.368 Å2 / ksol: 0.47 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1392 Å2-0 Å2-1.9244 Å2
2---9.9648 Å20 Å2
3---3.8255 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 21 73 1242
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021180
X-RAY DIFFRACTIONf_angle_d1.8571585
X-RAY DIFFRACTIONf_dihedral_angle_d16.111452
X-RAY DIFFRACTIONf_chiral_restr0.11188
X-RAY DIFFRACTIONf_plane_restr0.008197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96790.421420.30451215X-RAY DIFFRACTION81
1.9679-2.04670.30451550.28241344X-RAY DIFFRACTION89
2.0467-2.13980.28131450.24491440X-RAY DIFFRACTION93
2.1398-2.25260.24511580.20871419X-RAY DIFFRACTION94
2.2526-2.39370.26951640.21741407X-RAY DIFFRACTION94
2.3937-2.57840.27231580.22681461X-RAY DIFFRACTION95
2.5784-2.83770.34091600.23681475X-RAY DIFFRACTION96
2.8377-3.24790.24951680.23891491X-RAY DIFFRACTION98
3.2479-4.09040.23491720.20171527X-RAY DIFFRACTION100
4.0904-30.15960.22811640.2071540X-RAY DIFFRACTION99

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