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- PDB-6aw1: Crystal structure of CEACAM3 -

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Basic information

Entry
Database: PDB / ID: 6aw1
TitleCrystal structure of CEACAM3
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 3
KeywordsCELL ADHESION
Function / homology
Function and homology information


regulation of immune system process / specific granule membrane / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / Neutrophil degranulation / cell surface / signal transduction / plasma membrane
Similarity search - Function
Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Carcinoembryonic antigen-related cell adhesion molecule 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBonsor, D.A. / Sundberg, E.J.
CitationJournal: EMBO J. / Year: 2018
Title: TheHelicobacter pyloriadhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA.
Authors: Bonsor, D.A. / Zhao, Q. / Schmidinger, B. / Weiss, E. / Wang, J. / Deredge, D. / Beadenkopf, R. / Dow, B. / Fischer, W. / Beckett, D. / Wintrode, P.L. / Haas, R. / Sundberg, E.J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 3
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6979
Polymers24,0912
Non-polymers6067
Water1,18966
1
A: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2303
Polymers12,0461
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4676
Polymers12,0461
Non-polymers4225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Carcinoembryonic antigen-related cell adhesion molecule 3
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 3
B: Carcinoembryonic antigen-related cell adhesion molecule 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,39418
Polymers48,1824
Non-polymers1,21214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
Buried area7250 Å2
ΔGint-55 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.433, 94.433, 153.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-201-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 0 - 107 / Label seq-ID: 2 - 109

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 3 / Carcinoembryonic antigen CGM1


Mass: 12045.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM3, CD66D, CGM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40198

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Non-polymers , 5 types, 73 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.0M Ammonium Sulphate, 1% PEG 3350, 0.1M Bis Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2015 / Details: Flat Si Rh coated M0
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→80.46 Å / Num. obs: 20361 / % possible obs: 98.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1645 / Rpim(I) all: 0.748 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QSQ

2qsq


Resolution: 2.1→80.46 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / SU B: 12.373 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22302 1020 5 %RANDOM
Rwork0.20529 ---
obs0.20622 19328 98.39 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 54.236 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å2-0 Å20 Å2
2--1.26 Å2-0 Å2
3----2.51 Å2
Refinement stepCycle: 1 / Resolution: 2.1→80.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 37 66 1787
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191748
X-RAY DIFFRACTIONr_bond_other_d0.0020.021595
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9632369
X-RAY DIFFRACTIONr_angle_other_deg0.91633703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18125.38578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33915278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.58154
X-RAY DIFFRACTIONr_chiral_restr0.0840.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6872.767862
X-RAY DIFFRACTIONr_mcbond_other0.6872.767861
X-RAY DIFFRACTIONr_mcangle_it1.1634.1481074
X-RAY DIFFRACTIONr_mcangle_other1.1624.1471075
X-RAY DIFFRACTIONr_scbond_it0.6812.97884
X-RAY DIFFRACTIONr_scbond_other0.6812.97884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1144.3731296
X-RAY DIFFRACTIONr_long_range_B_refined4.95332.3331819
X-RAY DIFFRACTIONr_long_range_B_other4.95232.3871820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6594 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 70 -
Rwork0.349 1413 -
obs--98.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.15022.36490.47064.49881.62566.56150.27750.3067-0.1315-0.00230.0077-0.15-0.1764-0.5548-0.28520.17960.0467-0.00690.1750.03420.0197-27.70965.49115.3
23.9921-1.78771.28926.3772-2.97175.16530.08540.0589-0.15250.5302-0.11640.0066-0.26580.48940.0310.3929-0.0657-0.07120.1841-0.00580.0218-15.11466.265127.8191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 107
2X-RAY DIFFRACTION2B0 - 107

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