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- PDB-2c10: The structure of a truncated, soluble version of semicarbazide- s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c10 | ||||||||||||
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Title | The structure of a truncated, soluble version of semicarbazide- sensitive amine oxidase | ||||||||||||
![]() | MEMBRANE COPPER AMINE OXIDASE | ||||||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Function / homology | ![]() aliphatic amine oxidase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Jakobsson, E. / Kleywegt, G.J. | ||||||||||||
![]() | ![]() Title: Structure of human semicarbazide-sensitive amine oxidase/vascular adhesion protein-1. Authors: Jakobsson, E. / Nilsson, J. / Ogg, D. / Kleywegt, G.J. | ||||||||||||
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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 575 KB | Display | ![]() |
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PDB format | ![]() | 472.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2c11C ![]() 1ksiS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 81682.602 Da / Num. of mol.: 4 / Fragment: EXTRA-CELLULAR DOMAIN, RESIDUES 29-763 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 6 types, 20 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #5: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | ![]() Source method: isolated from a genetically manipulated source #7: Sugar | ChemComp-NAG / ![]() |
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-Non-polymers , 4 types, 583 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#8: Chemical | ChemComp-CA / #9: Chemical | ChemComp-CU / ![]() #10: Chemical | ChemComp-CL / ![]() #11: Water | ChemComp-HOH / | ![]() |
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-Details
Compound details | CELL ADHESION PROTEIN THAT IS INVOLVED IN THE BINDING OF LYMPHOCYTES TO PERIPHERAL LYMPH NODE ...CELL ADHESION PROTEIN THAT IS INVOLVED IN THE BINDING OF LYMPHOCYTE |
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Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5 Details: THE PROTEIN WAS CRYSTALLISED IN 0.1 M KBR, 0.1 M ACETATE PH 5, 38% PEG1000 AT 288 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 14, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→51.6 Å / Num. obs: 126698 / % possible obs: 100 % / Observed criterion σ(I): 3.2 / Redundancy: 5.2 % / Biso Wilson estimate: 48 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1KSI Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 14.748 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE LAST REFINEMENT ROUND WAS DONE AGAINST ALL DATA, RFREE VALUES ARE THE LAST RECORDED
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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: 37.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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