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- PDB-1rju: Crystal structure of a truncated form of yeast copper thionein -

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Basic information

Entry
Database: PDB / ID: 1rju
TitleCrystal structure of a truncated form of yeast copper thionein
ComponentsMetallothionein
KeywordsMETAL BINDING PROTEIN / Yeast Cu(I) metallothionein / Cu(I) metallothionein fragments / Cu(I)-thiolate
Function / homology
Function and homology information


detoxification of cadmium ion / detoxification of copper ion / response to copper ion / cadmium ion binding / superoxide dismutase activity / antioxidant activity / removal of superoxide radicals / copper ion binding / cytosol
Similarity search - Function
Metallothionein domain, yeast / Copper metallothionein superfamily / Yeast metallothionein / Metallothionein domain superfamily
Similarity search - Domain/homology
COPPER (I) ION / Copper metallothionein 1-1 / Copper metallothionein 1-1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 Å
AuthorsCalderone, V. / Dolderer, B. / Hartmann, H.J. / Echner, H. / Luchinat, C. / Del Bianco, C. / Mangani, S. / Weser, U.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: The Crystal Structure of Yeast Copper Thionein: the solution of a long lasting Enigma.
Authors: Calderone, V. / Dolderer, B. / Hartmann, H.J. / Echner, H. / Luchinat, C. / Del Bianco, C. / Mangani, S. / Weser, U.
#1: Journal: Eur.J.Biochem. / Year: 2000
Title: High resolution solution structure of the protein part of Cu7 metallothionein
Authors: Bertini, I. / Hartmann, H.J. / Klein, T. / Liu, G. / Luchinat, C. / Weser, U.
#2: Journal: J.Biol.Inorg.Chem. / Year: 2003
Title: The Cu(I)(7) cluster in yeast copper thionein survives major shortening of the polypeptide backbone as deduced from electronic absorption, circular dichroism, luminescence and (1)H NMR
Authors: Luchinat, C. / Dolderer, B. / Del Bianco, C. / Echner, H. / Hartmann, H.J. / Voelter, W. / Weser, U.
History
DepositionNov 20, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
V: Metallothionein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3569
Polymers3,8471
Non-polymers5088
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.167, 62.167, 62.167
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11V-77-

HOH

21V-78-

HOH

31V-79-

HOH

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Components

#1: Protein/peptide Metallothionein / Cu-MT / Copper chelatin


Mass: 3847.259 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The protein was Chemically synthesized. The sequence of the protein IS NATURALLY FOUND IN Saccharomyces cerevisiae (Baker's yeast).
References: UniProt: P07215, UniProt: P0CX80*PLUS
#2: Chemical
ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.6 Å3/Da / Density % sol: 52.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 250 mM KH2PO4, 1mM LiBr, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9192 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2003
RadiationMonochromator: Double crystal focusing monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionResolution: 1.44→27.84 Å / Num. all: 7922 / Num. obs: 7922 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.8 % / Biso Wilson estimate: 9.155 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 9.3
Reflection shellResolution: 1.44→1.52 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1117 / Rsym value: 0.358 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.44→27.84 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 0.568 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.056 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME EXTRA ELECTRON DENSITY CORRESPONDING TO 7 ATOMS HAS BEEN LEFT UNINTERPRETED SINCE NEITHER WATER MOLECULES NOR OTHER MOLECULES PRESENT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME EXTRA ELECTRON DENSITY CORRESPONDING TO 7 ATOMS HAS BEEN LEFT UNINTERPRETED SINCE NEITHER WATER MOLECULES NOR OTHER MOLECULES PRESENT IN THE CRYSTALLISATION SOLUTION COULD ACCOUNT FOR IT.
RfactorNum. reflection% reflectionSelection details
Rfree0.17072 634 8.1 %RANDOM
Rwork0.14482 ---
all0.14687 7239 --
obs0.14687 7239 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.889 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.052 Å0.056 Å
Refinement stepCycle: LAST / Resolution: 1.44→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms257 0 8 37 302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.02259
X-RAY DIFFRACTIONr_bond_other_d0.0650.02180
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.938345
X-RAY DIFFRACTIONr_angle_other_deg2.2373448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.006535
X-RAY DIFFRACTIONr_chiral_restr0.1430.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0480.02305
X-RAY DIFFRACTIONr_gen_planes_other0.1080.0235
X-RAY DIFFRACTIONr_nbd_refined0.2140.264
X-RAY DIFFRACTIONr_nbd_other0.270.2234
X-RAY DIFFRACTIONr_nbtor_other0.0950.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3370.213
X-RAY DIFFRACTIONr_mcbond_it2.4931.5179
X-RAY DIFFRACTIONr_mcangle_it3.5192284
X-RAY DIFFRACTIONr_scbond_it5.003380
X-RAY DIFFRACTIONr_scangle_it8.0324.561
X-RAY DIFFRACTIONr_rigid_bond_restr2.6842259
X-RAY DIFFRACTIONr_sphericity_free7.879247
X-RAY DIFFRACTIONr_sphericity_bonded4.6232257
LS refinement shellResolution: 1.44→1.478 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.176 40
Rwork0.139 526

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