+Open data
-Basic information
Entry | Database: PDB / ID: 4b92 | ||||||
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Title | Crystal structure of truncated human CRMP-5 soaked with Zn | ||||||
Components | DIHYDROPYRIMIDINASE-RELATED PROTEIN 5 | ||||||
Keywords | SIGNALING PROTEIN / NEUROGENESIS / PHOSPHOPROTEIN / CRMP / TIM BARREL / AXONAL OUTGROWTH / DEVELOPMENTAL PROTEIN | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / negative regulation of dendrite morphogenesis / CRMPs in Sema3A signaling / axon guidance / nervous system development / neuronal cell body / dendrite / signal transduction / protein-containing complex / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ponnusamy, R. / Lohkamp, B. | ||||||
Citation | Journal: J.Neurochem. / Year: 2013 Title: Insights Into the Oligomerization of Crmps: Crystal Structure of Human Collapsin Response Mediator Protein 5. Authors: Ponnusamy, R. / Lohkamp, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4b92.cif.gz | 190.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4b92.ent.gz | 151.2 KB | Display | PDB format |
PDBx/mmJSON format | 4b92.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/4b92 ftp://data.pdbj.org/pub/pdb/validation_reports/b9/4b92 | HTTPS FTP |
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-Related structure data
Related structure data | 4b90C 4b91SC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 8 - 481 / Label seq-ID: 9 - 482
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-Components
#1: Protein | Mass: 52953.496 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-483 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9BPU6 #2: Chemical | ChemComp-ZN / #3: 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: 2.28 Å3/Da / Density % sol: 46.08 % / Description: NONE |
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Crystal grow | pH: 5 / Details: 23% (V/V) PEG 400 MMT PH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.03873 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03873 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→39.3 Å / Num. obs: 23108 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7 % / Biso Wilson estimate: 70.549 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4B91 Resolution: 2.9→38.92 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.877 / SU B: 16.594 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 47.298 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→38.92 Å
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Refine LS restraints |
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