+Open data
-Basic information
Entry | Database: PDB / ID: 1lkx | ||||||
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Title | MOTOR DOMAIN OF MYOE, A CLASS-I MYOSIN | ||||||
Components | MYOSIN IE HEAVY CHAIN | ||||||
Keywords | CONTRACTILE PROTEIN / MYOSIN MOTOR DOMAIN / LEVER ARM / CONVERTER DOMAIN | ||||||
Function / homology | Function and homology information macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / leading edge membrane / vesicle transport along actin filament / early phagosome / myosin complex ...macropinocytic cup membrane / pseudopodium membrane / actin wave / macropinocytic cup cytoskeleton / chemotaxis to cAMP / macropinocytic cup / leading edge membrane / vesicle transport along actin filament / early phagosome / myosin complex / microfilament motor activity / phagocytic cup / phagocytosis, engulfment / cell leading edge / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / phagocytosis / actin filament polymerization / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calmodulin binding / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Dictyostelium discoideum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kollmar, M. / Durrwang, U. / Kliche, W. / Manstein, D.J. / Kull, F.J. | ||||||
Citation | Journal: EMBO J. / Year: 2002 Title: Crystal structure of the motor domain of a class-I myosin. Authors: Kollmar, M. / Durrwang, U. / Kliche, W. / Manstein, D.J. / Kull, F.J. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATES THE PUBLISHED SEQUENCE FOR DISTY MYOE IS INCORRECT IN A NUMBER OF PLACES. ...SEQUENCE AUTHOR STATES THE PUBLISHED SEQUENCE FOR DISTY MYOE IS INCORRECT IN A NUMBER OF PLACES. THE AUTHORS BELIEVE THEIR SEQUENCE TO BE MORE ACCURATE. THEY HAVE IDENTIFIED THE FOLLOWING CHANGES IN THEIR SEQUENCE/STRUCTURE FROM THE PUBLISHED ONE. THE DERIVED SEQUENCE OF MYOE WAS DIFFERENT FROM THE PUBLISHED SEQUENCE (URRUTIA ET AL., 1993, ACC. NR. L06805) IN 25 PLACES: WHILE SOME CHANGES CONCERNED NON-CONSERVED RESIDUES, ESPECIALLY IN THE REGIONS WHERE ADDITIONAL RESIDUES OR DELETIONS WERE FOUND, THE DERIVED SEQUENCE WAS IN BETTER AGREEMENT WITH THE AMINO ACID ALIGNMENT OF THE DICTYOSTELIUM MYOSINS. IN ONE REGION, A TEN RESIDUE SURFACE LOOP WAS FOUND TO BE COMPLETELY DIFFERENT. IN DETAIL, THE SEQUENCE CONTAINED THE FOLLOWING MODIFICATIONS COMPARED TO THE PUBLISHED ONE: D26E, R48T, I77M, I137L, R138D, F139 ABSENT, 140 ABSENT, N215D, L371I, S372I, I373N, V374C, H375T, R376T, G378K, T379G, P380 inserted, V427 inserted, R428 INSERTED, K429E, N440 INSERTED, N498I, D604V, I681N, R683T. THE AUTHORS STATE THEIR SEQUENCE COMPLETELY AGREES WITH THE FRAGMENT (AA270-1003) OBTAINED FROM THE DICTY GENOME SEQUENCING PROJECT. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lkx.cif.gz | 522.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lkx.ent.gz | 427.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/1lkx ftp://data.pdbj.org/pub/pdb/validation_reports/lk/1lkx | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 79165.273 Da / Num. of mol.: 4 / Fragment: Motor Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Plasmid: pDXA-3H / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: Q03479 #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-VO4 / #4: Chemical | ChemComp-ADP / #5: 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: 2.76 Å3/Da / Density % sol: 55.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 11% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 or 17 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3→50 Å / Num. obs: 54968 / Observed criterion σ(I): -3 | |||||||||||||||
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / % possible obs: 79.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.195 | |||||||||||||||
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.2 Å / % possible obs: 57.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 50 Å / Num. reflection obs: 54955 / Num. reflection Rfree: 5579 / % reflection Rfree: 9 % / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.228 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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