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- PDB-2qst: Crystal structure of the V39C mutant of the N-terminal domain of ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qst | ||||||
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Title | Crystal structure of the V39C mutant of the N-terminal domain of carcinoembryonic antigen (CEA) | ||||||
![]() | Carcinoembryonic antigen-related cell adhesion molecule 5 | ||||||
![]() | CELL ADHESION / Glycoprotein / GPI-anchor / Immunoglobulin domain / Lipoprotein / Membrane / Polymorphism | ||||||
Function / homology | ![]() GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane ...GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / negative regulation of apoptotic process / apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Le Trong, I. / Korotkova, N. / Moseley, S.L. / Stenkamp, R.E. | ||||||
![]() | ![]() Title: Binding of Dr adhesins of Escherichia coli to carcinoembryonic antigen triggers receptor dissociation. Authors: Korotkova, N. / Yang, Y. / Le Trong, I. / Cota, E. / Demeler, B. / Marchant, J. / Thomas, W.E. / Stenkamp, R.E. / Moseley, S.L. / Matthews, S. | ||||||
History |
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Remark 999 | Sequence The sequence was obtained from human cDNA and the authors confirmed that ALA is the ...Sequence The sequence was obtained from human cDNA and the authors confirmed that ALA is the correct sequence. However, the authors do not know if it is a mutation introduced by PCR or whether it is an SNP that results in the different amino acid. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
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PDB format | ![]() | 42.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Details | The two chains in the asymmetric unit (A,B) are parts of two biological units. A (x,y,z) and its crystallographically related partner, A'(x-y,-y,-z) form one dimer. B (x,y,z) and its crystallographically related partner, B' (2/3-x,1/3+y-x,1/3-z) form a similar, but slightly different, dimer. |
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Components
#1: Protein | Mass: 12435.001 Da / Num. of mol.: 2 / Fragment: N-terminal domain of CEA (UNP residues 34-110) / Mutation: V39C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.23 Å3/Da / Density % sol: 76.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 2.5 M NaCl, 0.1 M Tris-HCl, pH 7.0, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 12, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 11745 / Num. obs: 11745 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.9 % / Rmerge(I) obs: 0.228 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 1.2 / Num. unique all: 1152 / % possible all: 99.8 |
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Processing
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Refinement | Resolution: 2.9→41.89 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.111 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.441 / ESU R Free: 0.299 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.103 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→41.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.974 Å / Total num. of bins used: 20
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