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- PDB-4mt2: COMPARISON OF THE NMR SOLUTION STRUCTURE AND THE X-RAY CRYSTAL ST... -

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Basic information

Entry
Database: PDB / ID: 4mt2
TitleCOMPARISON OF THE NMR SOLUTION STRUCTURE AND THE X-RAY CRYSTAL STRUCTURE OF RAT METALLOTHIONEIN-2
ComponentsMETALLOTHIONEIN ISOFORM II
KeywordsMETALLOTHIONEIN
Function / homology
Function and homology information


Metallothioneins bind metals / negative regulation of growth / detoxification of copper ion / intracellular zinc ion homeostasis / cellular response to zinc ion / cellular response to cadmium ion / cellular response to copper ion / zinc ion binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Metallothionein Isoform II / Metallothionein Isoform II / Metallothionein, vertebrate / Metallothionein, vertebrate, metal binding site / Metallothionein domain superfamily, vertebrate / Metallothionein / Vertebrate metallothioneins signature. / Metallothionein domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
: / Metallothionein-2
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsRobbins, A.H. / Stout, C.D.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1992
Title: Comparison of the NMR solution structure and the x-ray crystal structure of rat metallothionein-2.
Authors: Braun, W. / Vasak, M. / Robbins, A.H. / Stout, C.D. / Wagner, G. / Kagi, J.H. / Wuthrich, K.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined Crystal Structure of Cd, Zn Metallothionein at 2.0 Angstroms Resolution
Authors: Robbins, A.H. / Mcree, D.E. / Collett, M.Williamson S.A. / Xoung, N.H. / Furey, W.F. / Wang, B.C. / Stout, C.D.
#2: Journal: Science / Year: 1986
Title: Crystal Structure Ofcd,Zn Metallothionein
Authors: Furey, W.F. / Robbins, A.H. / Clancy, L.L. / Winge, D.R. / Wang, B.-C. / Stout, C.D.
#3: Journal: J.Biol.Chem. / Year: 1983
Title: Single Crystals of Cadmium, Zinc Metallothionein
Authors: Melis, K.A. / Carter, D.C. / Stout, C.D. / Winge, D.R.
History
DepositionFeb 26, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
SupersessionMar 20, 2013ID: 2MT2
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_entry_details.has_protein_modification / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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
A: METALLOTHIONEIN ISOFORM II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8959
Polymers6,1791
Non-polymers7168
Water1,24369
1
A: METALLOTHIONEIN ISOFORM II
hetero molecules

A: METALLOTHIONEIN ISOFORM II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,79018
Polymers12,3592
Non-polymers1,43216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2710 Å2
ΔGint-102 kcal/mol
Surface area7820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)30.900, 30.900, 120.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein METALLOTHIONEIN ISOFORM II


Mass: 6179.380 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P04355
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTURN *T2* HAS A LEFT HANDED ALPHA CONFORMATION.
Has protein modificationY
Nonpolymer detailsTHE NUMBERING CONVENTION FOR THE FIVE CADMIUM ATOMS FOLLOWS THOSE USED IN THE NMR LITERATURE (SEE M. ...THE NUMBERING CONVENTION FOR THE FIVE CADMIUM ATOMS FOLLOWS THOSE USED IN THE NMR LITERATURE (SEE M. VASAK ET AL., J.MOL.BIOL. 196,711-719 (1987)). ZN1 AND ZN2 REPLACE CD2 AND CD3 IN THE CD(7) NMR STRUCTURES, RESPECTIVELY. BECAUSE NO ELECTRON DENSITY IS PRESENT AT THE ZINC POSITIONS IN AN ANOMALOUS DIFFERENCE FOURIER MAP, THE AUTHORS BELIEVE THAT LITTLE OR NO CADMIUM IS PRESENT AT THESE SITES. IN THESE MAPS, THE ELECTRON DENSITY FOR THE ISOLATED CADMIUM ATOM IN THE CDZN(2) CLUSTER IS COMPARABLE TO THAT OBSERVED AT EACH OF THE OTHER FOUR CADMIUM LOCATIONS. RESIDUE NA 1 IS OCTAHEDRALLY COORDINATED TO THE OXYGEN OF RESIDUES HOH 1, HOH 2, HOH 3 AND THE OXYGEN OF ALA 42' AND OG OF SER 45' IN A SYMMETRY RELATED MOLECULE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Melis, K.A., (1983) J.Biol.Chem., 258, 6255.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
21.0 Msodium formate1drop
30.2 Mpotassium phosphate1drop
45.0 Msodium formate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→5 Å / Rfactor Rwork: 0.197 / σ(F): 0
Details: THE STRUCTURE WAS SOLVED BY LOCATING THE FIVE CADMIUM ATOMS BY DIRECT METHODS. THE STARTING MODEL WAS A FIT OF THE CONSENSUS DOMAINS FROM THE 2-D NMR MODEL INTO AN ELECTRON DENSITY MAP ...Details: THE STRUCTURE WAS SOLVED BY LOCATING THE FIVE CADMIUM ATOMS BY DIRECT METHODS. THE STARTING MODEL WAS A FIT OF THE CONSENSUS DOMAINS FROM THE 2-D NMR MODEL INTO AN ELECTRON DENSITY MAP GENERATED FORM THE LOCATION OF THE CADMIUM POSITIONS. THE ANOMALOUS SCATTERING COMPONENTS OF CADMIUM ZINC AND SULFUR WERE INCLUDED IN THE REFINEMENT. DUE TO WEAK ELECTRON DENSITY, THE POSITIONS OF RESIDUES 1-2, 51-56, AND THE C-TERMINAL ALANINE SHOULD BE TREATED AS TENTATIVE. THE SIDE CHAINS OF LYSINES 20 AND 22 ARE ALSO UNRELIABLE.
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms403 0 8 69 480
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg3.5
Software
*PLUS
Name: XPLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.5

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