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- PDB-2qst: Crystal structure of the V39C mutant of the N-terminal domain of ... -

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Basic information

Entry
Database: PDB / ID: 2qst
TitleCrystal structure of the V39C mutant of the N-terminal domain of carcinoembryonic antigen (CEA)
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 5
KeywordsCELL ADHESION / Glycoprotein / GPI-anchor / Immunoglobulin domain / Lipoprotein / Membrane / Polymorphism
Function / homology
Function and homology information


GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane ...GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...: / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell adhesion molecule CEACAM5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLe Trong, I. / Korotkova, N. / Moseley, S.L. / Stenkamp, R.E.
CitationJournal: Mol.Microbiol. / Year: 2008
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
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Sequence 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 viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 5
B: Carcinoembryonic antigen-related cell adhesion molecule 5


Theoretical massNumber of molelcules
Total (without water)24,8702
Polymers24,8702
Non-polymers00
Water19811
1
A: Carcinoembryonic antigen-related cell adhesion molecule 5

A: Carcinoembryonic antigen-related cell adhesion molecule 5


Theoretical massNumber of molelcules
Total (without water)24,8702
Polymers24,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area1830 Å2
MethodPISA
2
B: Carcinoembryonic antigen-related cell adhesion molecule 5

B: Carcinoembryonic antigen-related cell adhesion molecule 5


Theoretical massNumber of molelcules
Total (without water)24,8702
Polymers24,8702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area1260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.228, 127.228, 166.940
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsThe 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 Carcinoembryonic antigen-related cell adhesion molecule 5 / Carcinoembryonic antigen / CEA / Meconium antigen 100 / CD66e antigen


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.) Homo sapiens (human) / Gene: CEACAM5, CEA / Plasmid: pET-21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06731
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.23 Å3/Da / Density % sol: 76.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 2.5 M NaCl, 0.1 M Tris-HCl, pH 7.0, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 12, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 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
RfactorNum. reflection% reflectionSelection details
Rfree0.25 556 4.7 %RANDOM
Rwork0.215 ---
obs0.215 11744 99.91 %-
all-11744 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.103 Å2
Baniso -1Baniso -2Baniso -3
1--2.51 Å2-1.26 Å20 Å2
2---2.51 Å20 Å2
3---3.77 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 0 11 1843
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221881
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9542556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3795226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.85325.10298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.58915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.824159
X-RAY DIFFRACTIONr_chiral_restr0.1010.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021449
X-RAY DIFFRACTIONr_nbd_refined0.2310.2886
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21316
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.23
X-RAY DIFFRACTIONr_mcbond_it0.6721.51144
X-RAY DIFFRACTIONr_mcangle_it1.20221830
X-RAY DIFFRACTIONr_scbond_it1.153826
X-RAY DIFFRACTIONr_scangle_it1.9954.5726
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 28 -
Rwork0.35 822 -
all-850 -
obs--99.3 %

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