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Yorodumi- PDB-1lot: CRYSTAL STRUCTURE OF THE COMPLEX OF ACTIN WITH VITAMIN D-BINDING ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lot | ||||||
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Title | CRYSTAL STRUCTURE OF THE COMPLEX OF ACTIN WITH VITAMIN D-BINDING PROTEIN | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / STRUCTURAL PROTEIN | ||||||
Function / homology | Function and homology information vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding ...vitamin transmembrane transporter activity / calcidiol binding / vitamin transport / Vitamin D (calciferol) metabolism / vitamin D metabolic process / vitamin D binding / cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / lysosomal lumen / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin binding / cell body / blood microparticle / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Head, J.F. / Swamy, N. / Ray, R. | ||||||
Citation | Journal: Biochemistry / Year: 2002 Title: Crystal structure of the complex between actin and human vitamin D-binding protein at 2.5 A resolution. Authors: Head, J.F. / Swamy, N. / Ray, R. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATES THE CONFLICT IS A VARIANT OF THE REFERENCE DATABASE SEQUENCE SWISS-PROT: P02774 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lot.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lot.ent.gz | 125.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lot.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lot_validation.pdf.gz | 483.3 KB | Display | wwPDB validaton report |
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Full document | 1lot_full_validation.pdf.gz | 510.8 KB | Display | |
Data in XML | 1lot_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 1lot_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lot ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lot | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 51277.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02774 |
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#2: Protein | Mass: 41875.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135 |
-Non-polymers , 4 types, 95 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-ATP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 58.8 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG8000, cacodylate, calcium acetate, glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 39295 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 12 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.5 / Num. unique all: 3754 / % possible all: 96.7 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 39585 / Num. measured all: 473796 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1ATN AND 1J78 Resolution: 2.5→50 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 52.1 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.223 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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