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Yorodumi- 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 | |||||||||
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Title | COMPARISON OF THE NMR SOLUTION STRUCTURE AND THE X-RAY CRYSTAL STRUCTURE OF RAT METALLOTHIONEIN-2 | |||||||||
Components | METALLOTHIONEIN ISOFORM II | |||||||||
Keywords | METALLOTHIONEIN | |||||||||
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 copper ion / cellular response to cadmium ion / zinc ion binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Rattus rattus (black rat) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | |||||||||
Authors | Robbins, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mt2.cif.gz | 21.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mt2.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mt2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/4mt2 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/4mt2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | ||||||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Compound details | TURN *T2* HAS A LEFT HANDED ALPHA CONFORMATI | Nonpolymer details | THE NUMBERING CONVENTION FOR THE FIVE CADMIUM ATOMS FOLLOWS THOSE USED IN THE NMR LITERATURE (SEE M. ...THE NUMBERING CONVENTION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % | |||||||||||||||||||||||||
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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
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 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 step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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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 |