+Open data
-Basic information
Entry | Database: PDB / ID: 2vkx | ||||||
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Title | Human NCAM, FN3 domains 1 and 2, M610R mutant | ||||||
Components | NEURAL CELL ADHESION MOLECULE | ||||||
Keywords | CELL ADHESION / ADHESION RECEPTOR | ||||||
Function / homology | Function and homology information regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / Signal transduction by L1 / NCAM signaling for neurite out-growth / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade ...regulation of semaphorin-plexin signaling pathway / commissural neuron axon guidance / NCAM1 interactions / ECM proteoglycans / epithelial to mesenchymal transition / Signal transduction by L1 / NCAM signaling for neurite out-growth / Interferon gamma signaling / virus receptor activity / RAF/MAP kinase cascade / collagen-containing extracellular matrix / cell adhesion / Golgi membrane / external side of plasma membrane / cell surface / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Carafoli, F. / Saffell, J.L. / Hohenester, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of the Tandem Fibronectin Type 3 Domains of Neural Cell Adhesion Molecule Authors: Carafoli, F. / Saffell, J.L. / Hohenester, E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vkx.cif.gz | 233.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vkx.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vkx_validation.pdf.gz | 490.4 KB | Display | wwPDB validaton report |
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Full document | 2vkx_full_validation.pdf.gz | 522.9 KB | Display | |
Data in XML | 2vkx_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 2vkx_validation.cif.gz | 60.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vkx ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vkx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23127.775 Da / Num. of mol.: 6 / Fragment: FN3 DOMAINS, RESIDUES 496-598,601-692 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: P13591 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, MET 611 TO ARG ENGINEERED RESIDUE IN CHAIN B, MET 611 TO ARG ...ENGINEERED | Sequence details | N-TERMINAL APLA AND C-TERMINAL AAAHHHHHH ARE VECTOR- DERIVED. QG (POSITIONS 599-600) OF P13591 ...N-TERMINAL APLA AND C-TERMINAL AAAHHHHHH ARE VECTOR- DERIVED. QG (POSITIONS 599-600) OF P13591 REPLACED BY R ( NATURAL MUSCLE- AND BRAIN-SPECIFIC SPLICE VARIANT). M610 REPLACED BY R (DESIGNED MUTATION). | |
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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: 3.06 Å3/Da / Density % sol: 59.48 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.12 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 21, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→20 Å / Num. obs: 44403 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.3 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NCAM FN3 DOMAIN PAIR, WILD-TYPE Resolution: 2.7→20 Å / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 37.8006 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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