+Open data
-Basic information
Entry | Database: PDB / ID: 4cnt | ||||||
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Title | CRYSTAL STRUCTURE OF WT HUMAN CRMP-4 | ||||||
Components | DIHYDROPYRIMIDINASE-LIKE 3 | ||||||
Keywords | SIGNALING PROTEIN / NEUROGENESIS / AXONAL OUTGROWTH / DEVELOPMENTAL PROTEIN | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / filamin binding / chondroitin sulfate binding / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / filamentous actin / cellular response to cytokine stimulus ...hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / filamin binding / chondroitin sulfate binding / actin crosslink formation / exocytic vesicle / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / positive regulation of filopodium assembly / filamentous actin / cellular response to cytokine stimulus / actin filament bundle assembly / response to axon injury / neuron development / negative regulation of cell migration / positive regulation of neuron projection development / SH3 domain binding / negative regulation of neuron projection development / lamellipodium / cell body / growth cone / synapse / extracellular space / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Ponnusamy, R. / Lohkamp, B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Crystal Structure of Human Crmp-4: Correction of Intensities for Lattice-Translocation Disorder Authors: Ponnusamy, R. / Lebedev, A. / Pahlow, S. / Lohkamp, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cnt.cif.gz | 722.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cnt.ent.gz | 599.8 KB | Display | PDB format |
PDBx/mmJSON format | 4cnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4cnt_validation.pdf.gz | 463.6 KB | Display | wwPDB validaton report |
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Full document | 4cnt_full_validation.pdf.gz | 478.8 KB | Display | |
Data in XML | 4cnt_validation.xml.gz | 63.2 KB | Display | |
Data in CIF | 4cnt_validation.cif.gz | 88.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/4cnt ftp://data.pdbj.org/pub/pdb/validation_reports/cn/4cnt | HTTPS FTP |
-Related structure data
Related structure data | 4cnsSC 4cnuC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 62049.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q8IXW6, UniProt: Q14195*PLUS #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-NA / | #4: 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: 2.13 Å3/Da / Density % sol: 42.4 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 15% (W/V) PEG 6000, 100 MM NAHEPES PH 7.5, 100 MM KCL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.07068 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 25, 2012 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.07068 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.66→43.79 Å / Num. obs: 61101 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.5 | |||||||||||||||
Reflection shell | Resolution: 2.66→2.72 Å / Redundancy: 3 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CNS Resolution: 2.65→55.97 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / SU B: 16.487 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.723 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→55.97 Å
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Refine LS restraints |
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