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- PDB-4mte: Zinc Uptake Regulator Complexed with Zinc and DNA -

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Basic information

Entry
Database: PDB / ID: 4mte
TitleZinc Uptake Regulator Complexed with Zinc and DNA
Components
  • (znuABC operator DNA) x 2
  • Zinc uptake regulation protein
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / winged-helix / DNA-binding regulatory protein / Helix-turn-helix / winged helix / Zinc regulated repressor / DNA binding / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich ...Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc uptake regulation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsGilston, B.A. / Mondragon, A. / O'Halloran, T.V.
CitationJournal: Plos Biol. / Year: 2014
Title: Structural and Mechanistic Basis of Zinc Regulation Across the E. coli Zur Regulon.
Authors: Gilston, B.A. / Wang, S. / Marcus, M.D. / Canalizo-Hernandez, M.A. / Swindell, E.P. / Xue, Y. / Mondragon, A. / O'Halloran, T.V.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc uptake regulation protein
B: Zinc uptake regulation protein
C: Zinc uptake regulation protein
D: Zinc uptake regulation protein
Y: znuABC operator DNA
Z: znuABC operator DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,94514
Polymers97,4226
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.324, 80.470, 98.770
Angle α, β, γ (deg.)90.00, 120.15, 90.00
Int Tables number5
Space group name H-MC121
DetailsA dimer of dimers is complexed with the duplex DNA molecule.

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Components

#1: Protein
Zinc uptake regulation protein / Zinc uptake regulator


Mass: 19282.213 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4046, JW5714, yjbK, zur / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AC51
#2: DNA chain znuABC operator DNA


Mass: 10206.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain znuABC operator DNA


Mass: 10086.547 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Sequence detailsMICRO-HETEROGENEITY IS OBSERVED. TWO ORIENTATIONS OF THE DNA WERE OBSERVED. THE GIVEN SEQUENCE ...MICRO-HETEROGENEITY IS OBSERVED. TWO ORIENTATIONS OF THE DNA WERE OBSERVED. THE GIVEN SEQUENCE CORRESPONDS TO ALTERNATE ID A.

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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: 3.41 Å3/Da / Density % sol: 63.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5 M Ammonium Sulfate, 0.1 M Citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2011 / Details: BERYLLIUM LENSES
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→36.4 Å / Num. all: 45429 / Num. obs: 45429 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 66.1 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.054 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5 / Rsym value: 0.331 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
SHARPphasing
REFMAC5.6.0117refinement
XDSdata scaling
XDSdata reduction
SCALAdata scaling
RefinementResolution: 2.5→36.34 Å / SU ML: 0.35 / σ(F): 1.05 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2569 4461 5.03 %
Rwork0.2175 --
obs0.2195 45418 99.56 %
all-45422 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 1969 8 0 6609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056966
X-RAY DIFFRACTIONf_angle_d0.9539888
X-RAY DIFFRACTIONf_dihedral_angle_d22.7892741
X-RAY DIFFRACTIONf_chiral_restr0.0481134
X-RAY DIFFRACTIONf_plane_restr0.003929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52850.3251100.30662632X-RAY DIFFRACTION94
2.5285-2.55820.34211340.30352809X-RAY DIFFRACTION100
2.5582-2.58940.36271800.29092825X-RAY DIFFRACTION100
2.5894-2.62210.38041390.28482825X-RAY DIFFRACTION100
2.6221-2.65660.37081310.27232860X-RAY DIFFRACTION100
2.6566-2.6930.3421680.26762799X-RAY DIFFRACTION100
2.693-2.73150.31591410.25272762X-RAY DIFFRACTION100
2.7315-2.77220.3031580.26342891X-RAY DIFFRACTION100
2.7722-2.81550.36591480.26452760X-RAY DIFFRACTION100
2.8155-2.86170.31521910.26712812X-RAY DIFFRACTION100
2.8617-2.9110.34381260.27452809X-RAY DIFFRACTION100
2.911-2.96390.3261610.2772810X-RAY DIFFRACTION100
2.9639-3.02090.30881610.27632807X-RAY DIFFRACTION100
3.0209-3.08250.29811670.25242805X-RAY DIFFRACTION100
3.0825-3.14950.40051550.26722825X-RAY DIFFRACTION100
3.1495-3.22270.29041780.24712776X-RAY DIFFRACTION100
3.2227-3.30330.28561340.23292830X-RAY DIFFRACTION100
3.3033-3.39250.23391720.24242791X-RAY DIFFRACTION100
3.3925-3.49230.24151090.22542873X-RAY DIFFRACTION100
3.4923-3.60490.24011500.22692781X-RAY DIFFRACTION100
3.6049-3.73360.28511510.2332841X-RAY DIFFRACTION100
3.7336-3.8830.27661390.21032838X-RAY DIFFRACTION100
3.883-4.05950.2141480.21252811X-RAY DIFFRACTION100
4.0595-4.27320.23771490.19352803X-RAY DIFFRACTION100
4.2732-4.54040.24151290.18042842X-RAY DIFFRACTION100
4.5404-4.89020.19891480.18792779X-RAY DIFFRACTION100
4.8902-5.38090.25941690.17842799X-RAY DIFFRACTION100
5.3809-6.15630.22891380.20322844X-RAY DIFFRACTION99
6.1563-7.74390.21931530.19652740X-RAY DIFFRACTION99
7.7439-36.3440.16991240.16682772X-RAY DIFFRACTION97

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