[English] 日本語
Yorodumi- PDB-5cpv: RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cpv | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | RESTRAINED LEAST SQUARES REFINEMENT OF NATIVE (CALCIUM) AND CADMIUM-SUBSTITUTED CARP PARVALBUMIN USING X-RAY CRYSTALLOGRAPHIC DATA AT 1.6-ANGSTROMS RESOLUTION | |||||||||
Components | CALCIUM-BINDING PARVALBUMIN B | |||||||||
Keywords | CALCIUM BINDING | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cyprinus carpio (common carp) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Swain, A.L. / Kretsinger, R.H. / Amma, E.L. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 1989 Title: Restrained least squares refinement of native (calcium) and cadmium-substituted carp parvalbumin using X-ray crystallographic data at 1.6-A resolution. Authors: Swain, A.L. / Kretsinger, R.H. / Amma, E.L. #1: Journal: Inorg.Chim.Acta. / Year: 1989 Title: The Coordination Polyhedron of Ca2+,Cd2+ in Parvalbumin Authors: Swain, A.L. / Amma, E.L. #2: Journal: J.Mol.Biol. / Year: 1975 Title: Refinement of the Structure of Carp Muscle Calcium-Binding Parvalbumin by Model Building and Difference Fourier Analysis Authors: Moews, P.C. / Kretsinger, R.H. #3: Journal: J.Mol.Biol. / Year: 1975 Title: Terbium Replacement of Calcium in Carp Muscle Calcium-Binding Parvalbumin,an X-Ray Crystallographic Study Authors: Moews, P.C. / Kretsinger, R.H. #4: Journal: Science / Year: 1975 Title: Troponin and Parvalbumin Calcium Binding Regions Predicted in Myosin Light Chain and T4 Lysozyme Authors: Tufty, R.M. / Kretsinger, R.H. #5: Journal: Perspectives in Membrane Biology / Year: 1974 Title: Calcium Binding Proteins and Natural Membranes Authors: Kretsinger, R.H. #6: Journal: Adv.Exp.Med.Biol. / Year: 1974 Title: The Coordination of Calcium Ions by Carp Muscle Calcium-Binding Proteins A,B,and C Authors: Coffee, C.J. / Bradshaw, R.A. / Kretsinger, R.H. #7: Journal: J.Biol.Chem. / Year: 1973 Title: Carp Muscle Calcium-Binding Protein, I.Characterization of the Tryptic Peptides and the Complete Amino Acid Sequence of Component B Authors: Coffee, C.J. / Bradshaw, R.A. #8: Journal: J.Biol.Chem. / Year: 1973 Title: Carp Muscle Calcium-Binding Protein, II.Structure Determination and General Description Authors: Kretsinger, R.H. / Nockolds, C.E. #9: Journal: J.Biol.Chem. / Year: 1973 Title: Carp Muscle Calcium-Binding Protein, III.Phase Refinement Using the Tangent Formula Authors: Hendrickson, W.A. / Karle, J. #10: Journal: Nature New Biol. / Year: 1972 Title: Gene Duplication in Carp Muscle Calcium Binding Protein Authors: Mclachlan, A.D. #11: Journal: Nature New Biol. / Year: 1972 Title: Gene Triplication Deduced from the Tertiary Structure of a Muscle Calcium Binding Protein Authors: Kretsinger, R.H. #12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1972 Title: Structure of a Calcium Binding Carp Myogen Authors: Nockolds, C.E. / Kretsinger, R.H. / Coffee, C.J. / Bradshaw, R.A. #13: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972 Title: The Structure of a Calcium-Binding Protein from Carp Muscle Authors: Kretsinger, R.H. / Nockolds, C.E. / Coffee, C.J. / Bradshaw, R.A. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5cpv.cif.gz | 31.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5cpv.ent.gz | 24 KB | Display | PDB format |
PDBx/mmJSON format | 5cpv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cp/5cpv ftp://data.pdbj.org/pub/pdb/validation_reports/cp/5cpv | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: HOH 132 IS THE SEVENTH LIGAND FOR CA 109. |
-Components
#1: Protein | Mass: 11476.829 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyprinus carpio (common carp) / References: UniProt: P02618 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.09 % |
---|---|
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, sitting drop |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.6→10 Å / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 10879 / Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(I): 3 / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.5 Å2 |