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Yorodumi- PDB-1vrk: THE 1.9 ANGSTROM STRUCTURE OF E84K-CALMODULIN RS20 PEPTIDE COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vrk | ||||||
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Title | THE 1.9 ANGSTROM STRUCTURE OF E84K-CALMODULIN RS20 PEPTIDE COMPLEX | ||||||
Components |
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Keywords | COMPLEX(CALCIUM-BINDING PROTEIN/PEPTIDE) / CALMODULIN / CALCIUM BINDING / HELIX-LOOP-HELIX / SIGNALLING / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) / COMPLEX(CALCIUM-BINDING PROTEIN-PEPTIDE) complex | ||||||
Function / homology | Function and homology information tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / phosphorylation / ATP binding ...tonic smooth muscle contraction / myosin-light-chain kinase / myosin light chain kinase activity / muscle structure development / cleavage furrow / stress fiber / lamellipodium / calmodulin binding / phosphorylation / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Weigand, S. / Anderson, W.F. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Analysis of the functional coupling between calmodulin's calcium binding and peptide recognition properties. Authors: Mirzoeva, S. / Weigand, S. / Lukas, T.J. / Shuvalova, L. / Anderson, W.F. / Watterson, D.M. #1: Journal: Science / Year: 1992 Title: Target Enzyme Recognition by Calmodulin: 2.4 A Structure of a Calmodulin-Peptide Complex Authors: Meador, W.E. / Means, A.R. / Quiocho, F.A. | ||||||
History |
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Remark 650 | HELIX THE STRUCTURAL CONSEQUENCE OF THE E84K MUTATION RELATIVE TO THE WILD TYPE STRUCTURE ...HELIX THE STRUCTURAL CONSEQUENCE OF THE E84K MUTATION RELATIVE TO THE WILD TYPE STRUCTURE (REFERENCE 1 ABOVE) IS AN ALTERATION OF THE RESIDUE 84 CONFORMATION AND A FIVE DEGREE MOVEMENT OF HELIX E (HELIX 5) AWAY FROM THE PEPTIDE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vrk.cif.gz | 49.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vrk.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 1vrk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vrk_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1vrk_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 1vrk_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 1vrk_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vrk ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vrk | HTTPS FTP |
-Related structure data
Related structure data | 1cdlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16642.338 Da / Num. of mol.: 1 / Mutation: E84K Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Description: CONSENSUS SEQUENCE FROM A NUMBER OF SOURCES; / Plasmid: PVUCH-1 / Production host: Escherichia coli (E. coli) / Strain (production host): UT481 / References: GenBank: 3561059 | ||||||
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#2: Protein/peptide | Mass: 2327.696 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TRP 4 IS NE-FORMYLATED / References: UniProt: P11799*PLUS, EC: 2.7.1.117 | ||||||
#3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Compound details | THE ENHANCEMENT OF CALMODULIN'S CALCIUM BINDING BY SMOOTH MUSCLE/NONMUSCLE MYOSIN LIGHT CHAIN ...THE ENHANCEMEN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 1, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→18.2 Å / Num. obs: 11190 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.0649 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CDL: SECOND COMPLEX (SEGID B AND F) OF THE ASYMMETRIC UNIT Resolution: 1.9→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 30.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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