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- PDB-4whc: Human CEACAM6 N-domain -

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Basic information

Entry
Database: PDB / ID: 4whc
TitleHuman CEACAM6 N-domain
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 6
KeywordsPROTEIN BINDING / dimer / receptor / CEACAM
Function / homology
Function and homology information


positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / positive regulation of heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / azurophil granule membrane / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / positive regulation of cell migration ...positive regulation of endothelial cell-matrix adhesion via fibronectin / Fibronectin matrix formation / positive regulation of heterotypic cell-cell adhesion / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / azurophil granule membrane / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / positive regulation of cell migration / apical plasma membrane / protein heterodimerization activity / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular space / 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 CEACAM6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.705 Å
AuthorsPrive, G.G. / Kirouac, K.N.
CitationJournal: To Be Published
Title: Human CEACAM6 N-domain
Authors: Prive, G.G. / Kirouac, K.N.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 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_struct_oper_list / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

Downloads & links

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 6
B: Carcinoembryonic antigen-related cell adhesion molecule 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8923
Polymers23,8262
Non-polymers651
Water1629
1
A: Carcinoembryonic antigen-related cell adhesion molecule 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9792
Polymers11,9131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carcinoembryonic antigen-related cell adhesion molecule 6


Theoretical massNumber of molelcules
Total (without water)11,9131
Polymers11,9131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.912, 91.912, 60.359
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-301-

HOH

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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 2 - 106 / Label seq-ID: 3 - 107

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

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 6 / Non-specific crossreacting antigen / Normal cross-reacting antigen


Mass: 11913.239 Da / Num. of mol.: 2 / Fragment: N-domain (UNP residues 34-141)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM6, NCA / Production host: Escherichia coli (E. coli) / References: UniProt: P40199
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 20% PEG 3000, 100 mM Imidazole pH 8.0, 200 mM ZnAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30.1 Å / Num. obs: 8009 / % possible obs: 99.4 % / Redundancy: 4.5 % / Net I/σ(I): 35.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.705→30.1 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 28.518 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.014 / ESU R Free: 0.308 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2266 803 10 %RANDOM
Rwork0.1882 7202 --
obs0.1922 8005 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 100.22 Å2 / Biso mean: 60.811 Å2 / Biso min: 46.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å2-0 Å2
2---0.07 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2.705→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 1 9 1686
Biso mean--70.03 82.34 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191712
X-RAY DIFFRACTIONr_bond_other_d0.0030.021599
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9512337
X-RAY DIFFRACTIONr_angle_other_deg0.91233667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5735213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23325.36682
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64915266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.458156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2265
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211993
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02401
X-RAY DIFFRACTIONr_mcbond_it1.8376.024858
X-RAY DIFFRACTIONr_mcbond_other1.8356.025857
X-RAY DIFFRACTIONr_mcangle_it2.8699.0381069
Refine LS restraints NCS

Ens-ID: 1 / Number: 6006 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.705→2.776 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 59 -
Rwork0.301 523 -
all-582 -
obs--99.32 %
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)
17.40991.1882-3.76094.9821-1.15067.2899-0.54350.2835-0.48230.07360.39620.26280.4325-0.57750.14730.17740.03780.00690.1462-0.05480.11178.54895.0736.657
24.15180.76060.29646.86720.78154.680.0646-0.14590.20630.21960.07560.01620.0778-0.0447-0.14020.3546-0.01830.08060.1421-0.14890.17781.67675.264-4.232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 107
2X-RAY DIFFRACTION2B0 - 107

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