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- PDB-4jgj: Crystal structure of the Ig-like D1 domain from mouse Carcinoembr... -

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Basic information

Entry
Database: PDB / ID: 4jgj
TitleCrystal structure of the Ig-like D1 domain from mouse Carcinoembryogenic antigen-related cell adhesion molecule 15 (CEACAM15) [PSI-NYSGRC-005691]
Components
  • Carcinoembryonic antigen-related cell adhesion molecule 15
  • Unknown peptide
KeywordsIMMUNE SYSTEM / CEACAM15 / Ig-like D1 domain / Ig superfamily / Cell adhesion / Structural genomics / PSI-Biology / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


Immunoglobulin I-set / Immunoglobulin I-set 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 I-set / Immunoglobulin I-set 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 15 / Carcinoembryonic antigen-related cell adhesion molecule 15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6508 Å
AuthorsKumar, P.R. / Bonanno, J. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. ...Kumar, P.R. / Bonanno, J. / Ahmed, M. / Banu, R. / Bhosle, R. / Calarese, D. / Celikigil, A. / Chamala, S. / Chan, M.K. / Chowdhury, S. / Fiser, A. / Garforth, S. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Love, J. / Patel, H. / Seidel, R. / Stead, M. / Toro, R. / Nathenson, S.G. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: to be published
Title: Crystal structure of the Ig-like D1 domain of CEACAM15 from Mus musculus [NYSGRC-005691]
Authors: Kumar, P.R. / Bonanno, J. / Nathenson, S.G. / Almo, S.C.
History
DepositionMar 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 15
B: Carcinoembryonic antigen-related cell adhesion molecule 15
X: Unknown peptide
Y: Unknown peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4006
Polymers29,9584
Non-polymers4422
Water21612
1
A: Carcinoembryonic antigen-related cell adhesion molecule 15
B: Carcinoembryonic antigen-related cell adhesion molecule 15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0034
Polymers28,5602
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-6 kcal/mol
Surface area10480 Å2
MethodPISA
2
X: Unknown peptide


  • defined by author&software
  • 699 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6991
Polymers6991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
Y: Unknown peptide


  • defined by author&software
  • 699 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)6991
Polymers6991
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.168, 101.168, 75.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 15


Mass: 14280.100 Da / Num. of mol.: 2 / Fragment: UNP Reesidues 26-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CEACAM-15, Ceacam15 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: A0JLX4, UniProt: A0A0B4J1L0*PLUS
#2: Protein/peptide Unknown peptide


Mass: 698.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Unknown polpypeptides, probably arising from cloning artifacts at the N and/or C-terminus.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CEACAM-15 / Plasmid: pIEX / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS X & Y IN THE STRUCTURE ARE POLYPEPTIDES WHICH THE AUTHORS BELIEVE REPRESENTS EITHER THE N OR ...CHAINS X & Y IN THE STRUCTURE ARE POLYPEPTIDES WHICH THE AUTHORS BELIEVE REPRESENTS EITHER THE N OR C-TERMINAL STRETCH CORRESPONDING TO THE CLONING ARTIFACTS AT EITHER TERMINI OF THE CEACAM-15 CONSTRUCT. HOWEVER THE POLYPEPTIDE CONNECTIVITY TO EITHER CHAIN A OR B IS NOT WELL DEFINED. THE SIDE CHAIN DENSITIES OF X & Y WERE ALSO NOT CLEAR AND HENCE MODELED AS POLY-ALANINE. THEREFORE, WE LIKE TO CALL CHAINS X & Y AS UNKNOWN PEPTIDES.

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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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 7
Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Sodium Chloride, 0.1M Sodium Citrate:Citric Acid (pH 5.5), 40%(v/v) 1,2-Propanediol); Cryoprotection (Reservoir + ...Details: Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.2M Sodium Chloride, 0.1M Sodium Citrate:Citric Acid (pH 5.5), 40%(v/v) 1,2-Propanediol); Cryoprotection (Reservoir + final concentration of 20%(v/v) DMSO), Sitting Drop Vapor Diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.5
ReflectionResolution: 2.65→50 Å / Num. all: 8403 / Num. obs: 8392 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.057 / Χ2: 0.954 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.65-2.76.84010.9291100
2.7-2.747.44310.911199.8
2.74-2.87.54180.9161100
2.8-2.857.74160.941199.5
2.85-2.927.74150.966199.8
2.92-2.987.74330.97711000.82
2.98-3.067.74050.97711000.593
3.06-3.147.74290.97811000.44
3.14-3.237.84240.995199.80.337
3.23-3.347.74161.0211000.219
3.34-3.467.74140.97111000.14
3.46-3.67.74150.97211000.114
3.6-3.767.74351.04811000.097
3.76-3.967.74141.01311000.077
3.96-4.217.74261.03111000.055
4.21-4.537.74271.05611000.042
4.53-4.997.64131.06611000.036
4.99-5.717.64240.84211000.04
5.71-7.197.54150.79911000.036
7.19-507.84210.667199.30.026

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6508→37.92 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8224 / σ(F): 2 / Phase error: 25.32 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 320 4.65 %RANDOM
Rwork0.1953 ---
obs0.2041 6884 82.31 %-
all-8403 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.16 Å2 / Biso mean: 44.8829 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.6508→37.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 28 12 1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091800
X-RAY DIFFRACTIONf_angle_d1.2772411
X-RAY DIFFRACTIONf_chiral_restr0.07279
X-RAY DIFFRACTIONf_plane_restr0.006294
X-RAY DIFFRACTIONf_dihedral_angle_d16.286639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6508-3.33690.26281070.20462575268262
3.3369-19.09820.23492040.19993978418295
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)
10.5037-0.1086-0.60741.0521-0.1960.8310.4298-0.1070.10790.26770.0633-0.3048-0.04880.07210.45570.096-0.2096-0.18110.697-0.10510.524576.83973.795511.0099
23.079-0.8588-0.54174.07370.57352.61650.55830.01070.71960.645-0.4907-0.15770.129-0.07250.07820.21-0.1393-0.0160.5004-0.03310.380667.011772.069811.9217
30.5266-0.366-0.8211.60430.12791.40340.4931-0.12820.66840.1358-0.0857-0.13560.0677-0.0745-0.01190.1573-0.144-0.14580.69960.07560.693676.510976.966711.8447
40.2974-0.50490.37433.30370.41470.9418-0.17810.5814-0.33830.4580.06250.68350.18920.0325-0.01170.3977-0.2162-0.05610.4547-0.15510.527449.456658.549213.4913
51.4161-0.19070.12952.2174-0.20151.0680.27390.20220.26350.4347-0.21120.5550.2378-0.1072-0.06850.3139-0.3661-0.1050.6238-0.06610.481255.828565.829812.1899
60.5616-0.50540.14221.9715-0.60330.73990.37450.0862-0.31720.06560.06040.62190.1603-0.2558-0.04530.4826-0.4205-0.02610.7809-0.09670.621847.002559.977512.6023
70.0867-0.02390.00460.04330.0560.08780.0502-0.06710.02210.0661-0.03260.0274-0.01140.0013-0.07870.4598-0.3224-0.18290.5689-0.1540.790989.413874.772423.3606
80.4378-0.0378-0.77070.03950.05041.36380.09380.107-0.01440.0335-0.01770.07580.0574-0.054-0.05110.4648-0.3282-0.23880.7465-0.17050.78742.425847.43290.3777
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 111 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 137)A0
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 65 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 111 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 112 through 137 )B0
7X-RAY DIFFRACTION7chain 'X' and (resid 1 through 8)X0
8X-RAY DIFFRACTION8chain 'Y' and (resid 101 through 108)Y0

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