+Open data
-Basic information
Entry | Database: PDB / ID: 1kcx | ||||||
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Title | X-ray structure of NYSGRC target T-45 | ||||||
Components | DIHYDROPYRIMIDINASE RELATED PROTEIN-1 | ||||||
Keywords | SIGNALING PROTEIN / alpha/beta barrel / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information negative regulation of actin filament binding / CRMPs in Sema3A signaling / filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / semaphorin-plexin signaling pathway / axon guidance / phosphoprotein binding / spindle / microtubule cytoskeleton organization / actin cytoskeleton ...negative regulation of actin filament binding / CRMPs in Sema3A signaling / filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / semaphorin-plexin signaling pathway / axon guidance / phosphoprotein binding / spindle / microtubule cytoskeleton organization / actin cytoskeleton / negative regulation of neuron projection development / midbody / growth cone / perikaryon / centrosome / dendrite / neuronal cell body / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å | ||||||
Authors | Deo, R.C. / Schmidt, E.F. / Strittmatter, S.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structural bases for CRMP function in plexin-dependent semaphorin3A signaling Authors: Deo, R.C. / Schmidt, E.F. / Elhabazi, A. / Togashi, H. / Burley, S.K. / Strittmatter, S.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kcx.cif.gz | 207.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kcx.ent.gz | 164.4 KB | Display | PDB format |
PDBx/mmJSON format | 1kcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kc/1kcx ftp://data.pdbj.org/pub/pdb/validation_reports/kc/1kcx | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56371.977 Da / Num. of mol.: 2 / Fragment: RESIDUES 8-525 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: crmp1 (8-525) / Plasmid: pgex6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): ut5600 / References: UniProt: P97427 #2: 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: 3.27 Å3/Da / Density % sol: 62.39 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: isopropanol, tris, ammonium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.984 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2000 |
Radiation | Monochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→24 Å / Num. all: 78239 / Num. obs: 78239 / % possible obs: 93.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.12→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 4 / Num. unique all: 6361 / Rsym value: 0.313 / % possible all: 76.8 |
Reflection | *PLUS Lowest resolution: 24 Å / Num. measured all: 753778 |
Reflection shell | *PLUS % possible obs: 76.8 % / Mean I/σ(I) obs: 1.23 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.12→20 Å / σ(F): 2 / Stereochemistry target values: engh & huber
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Refinement step | Cycle: LAST / Resolution: 2.12→20 Å
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Refinement | *PLUS Lowest resolution: 24 Å / % reflection Rfree: 5 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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