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- PDB-4mtd: Zinc Uptake Regulator Complexed With Zinc AND DNA -

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Basic information

Entry
Database: PDB / ID: 4mtd
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 1.2Feb 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
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-110 kcal/mol
Surface area38870 Å2
MethodPISA
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

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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: 3.45 Å3/Da / Density % sol: 64.37 %
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: 2.48→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 % / Rmerge(I) obs: 0.046 / Rsym value: 0.054 / Net I/σ(I): 19.4
Reflection shellResolution: 2.48→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
XDSdata scaling
SHARPphasing
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
RefinementResolution: 2.5→36.34 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.89 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.334 / ESU R Free: 0.258 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27125 2290 5 %RANDOM
Rwork0.23417 ---
obs0.23602 43139 99.73 %-
all-42672 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.422 Å2
Baniso -1Baniso -2Baniso -3
1-5.2 Å2-0 Å20.06 Å2
2---2.84 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4632 1355 8 0 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0176263
X-RAY DIFFRACTIONr_bond_other_d0.0010.025328
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.7638742
X-RAY DIFFRACTIONr_angle_other_deg0.8963.00312290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82424.404218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16715832
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3061533
X-RAY DIFFRACTIONr_chiral_restr0.0630.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026175
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021339
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7486.3062390
X-RAY DIFFRACTIONr_mcbond_other2.7486.3042389
X-RAY DIFFRACTIONr_mcangle_it4.6379.4462981
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1816.6933873
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 141 -
Rwork0.309 3120 -
obs--98.34 %

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