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Open data
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Basic information
Entry | Database: PDB / ID: 4cns | ||||||
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Title | Crystal structure of truncated human CRMP-4 | ||||||
![]() | DIHYDROPYRIMIDINASE-LIKE 3 | ||||||
![]() | SIGNALING PROTEIN / NEUROGENESIS / AXONAL OUTGROWTH / DEVELOPMENTAL PROTEIN | ||||||
Function / homology | ![]() 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 / cellular response to cytokine stimulus / filamentous actin ...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 / cellular response to cytokine stimulus / filamentous actin / actin filament bundle assembly / response to axon injury / neuron development / negative regulation of cell migration / positive regulation of neuron projection development / SH3 domain binding / lamellipodium / negative regulation of neuron projection development / cell body / growth cone / synapse / extracellular space / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ponnusamy, R. / Lohkamp, B. | ||||||
![]() | ![]() Title: Crystal Structure of Human Crmp-4: Correction of Intensities for Lattice-Translocation Disorder Authors: Ponnusamy, R. / Lebedev, A. / Pahlow, S. / Lohkamp, B. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 713 KB | Display | ![]() |
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PDB format | ![]() | 592.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 471.2 KB | Display | ![]() |
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Full document | ![]() | 478.3 KB | Display | |
Data in XML | ![]() | 68.3 KB | Display | |
Data in CIF | ![]() | 97.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cntC ![]() 4cnuC ![]() 4b91S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given) |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 52631.500 Da / Num. of mol.: 4 / Fragment: RESIDUES 13-490 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 608 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 30% (W/V) PEG 3350, 100 MM NA TARTRATE, 100 MM BIS-TRIS PROPANE 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.04088 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→31.21 Å / Num. obs: 75030 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.4 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4B91 Resolution: 2.4→30.99 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.89 / SU B: 15.526 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.593 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 19.372 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30.99 Å
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