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- PDB-4b3z: Structure of the human collapsin response mediator protein-1, a l... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4b3z | ||||||
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Title | Structure of the human collapsin response mediator protein-1, a lung cancer suppressor | ||||||
![]() | DIHYDROPYRIMIDINASE-RELATED PROTEIN 1 | ||||||
![]() | HYDROLASE / SEMAPHORIN 3A / TIM BARREL / NON-SMALL-CELL LUNG CANCER / LUNG CANCER SUPPRESSOR | ||||||
Function / homology | ![]() negative regulation of actin filament binding / filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / axon guidance / microtubule cytoskeleton organization / spindle / negative regulation of neuron projection development / nervous system development ...negative regulation of actin filament binding / filamin binding / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / axon guidance / microtubule cytoskeleton organization / spindle / negative regulation of neuron projection development / nervous system development / midbody / growth cone / perikaryon / centrosome / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, S.H. / Lin, Y.H. / Huang, S.F. / Niou, Y.K. / Huang, L.L. / Chen, Y.J. | ||||||
![]() | ![]() Title: Structure of Human Collapsin Response Mediator Protein 1: A Possible Role of its C-Terminal Tail. Authors: Liu, S.H. / Huang, S.F. / Hsu, Y.L. / Pan, S.H. / Chen, Y.J. / Lin, Y.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 359.8 KB | Display | ![]() |
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PDB format | ![]() | 294.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 450.5 KB | Display | |
Data in XML | ![]() | 60.6 KB | Display | |
Data in CIF | ![]() | 82.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 62256.602 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.9 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN SOLUTION AT 10 MG/ML IN 20 MM TRIS-HCL WITH 150 MM NACL, PH 7.5 AND THE WELL SOLUTION (50 MM AMMONIUM SULFATE, 50 MM SODIUM CITRATE, 12-15% PEG 8000) IN A 1:1 RATIO |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.549 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 42140 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 58.03 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.38 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.3 / % possible all: 91.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 1KCX AND 2VM8 Resolution: 3.05→39.184 Å / SU ML: 0.69 / σ(F): 1.39 / Phase error: 22.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 9.595 Å2 / ksol: 0.283 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.69 Å2
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Refinement step | Cycle: LAST / Resolution: 3.05→39.184 Å
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Refine LS restraints |
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LS refinement shell |
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