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- PDB-4y89: Crystal structure of the N-terminal domain of CEACAM7 -

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Basic information

Entry
Database: PDB / ID: 4y89
TitleCrystal structure of the N-terminal domain of CEACAM7
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 7
KeywordsCELL ADHESION
Function / homology
Function and homology information


: / Post-translational modification: synthesis of GPI-anchored proteins / apical plasma membrane / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like ...Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 7 / Carcinoembryonic antigen-related cell adhesion molecule 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsBonsor, D.A. / Sundberg, E.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the N-terminal dimerization domain of CEACAM7.
Authors: Bonsor, D.A. / Beckett, D. / Sundberg, E.J.
History
DepositionFeb 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 7
B: Carcinoembryonic antigen-related cell adhesion molecule 7
C: Carcinoembryonic antigen-related cell adhesion molecule 7
D: Carcinoembryonic antigen-related cell adhesion molecule 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9307
Polymers49,8234
Non-polymers1063
Water4,846269
1
A: Carcinoembryonic antigen-related cell adhesion molecule 7
C: Carcinoembryonic antigen-related cell adhesion molecule 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9473
Polymers24,9122
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-7 kcal/mol
Surface area10190 Å2
MethodPISA
2
B: Carcinoembryonic antigen-related cell adhesion molecule 7
D: Carcinoembryonic antigen-related cell adhesion molecule 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9834
Polymers24,9122
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-9 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.623, 64.886, 103.164
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carcinoembryonic antigen-related cell adhesion molecule 7


Mass: 12455.838 Da / Num. of mol.: 4 / Fragment: IgV domain (UNP residues 34-142)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0A0MTT6, UniProt: Q14002*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18% PEG 8000, 0.1 M Tris, pH 8.5, 0.2M Magnesium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.47→103.16 Å / Num. obs: 71599 / % possible obs: 98.2 % / Redundancy: 2.9 % / Rsym value: 0.105 / Net I/σ(I): 28
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 1.57 / % possible all: 82.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QSQ

2qsq


Resolution: 1.47→103.16 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.972 / SU B: 5.204 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 3613 5 %RANDOM
Rwork0.1428 ---
obs0.1455 67967 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.64 Å2 / Biso mean: 27.343 Å2 / Biso min: 14.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-3.82 Å2
2---0.59 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.47→103.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3522 0 3 269 3794
Biso mean--41.91 39.54 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193615
X-RAY DIFFRACTIONr_bond_other_d0.0010.023361
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.9144932
X-RAY DIFFRACTIONr_angle_other_deg0.99437659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54225.073205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53115561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.8481516
X-RAY DIFFRACTIONr_chiral_restr0.1390.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024251
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02927
X-RAY DIFFRACTIONr_mcbond_it3.2762.2711734
X-RAY DIFFRACTIONr_mcbond_other3.2772.271733
X-RAY DIFFRACTIONr_mcangle_it3.8613.4342161
X-RAY DIFFRACTIONr_rigid_bond_restr5.7336976
X-RAY DIFFRACTIONr_sphericity_free36.9025106
X-RAY DIFFRACTIONr_sphericity_bonded25.34557056
LS refinement shellResolution: 1.471→1.509 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 226 -
Rwork0.28 4156 -
all-4382 -
obs--81.56 %

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