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- PDB-5vst: Crystal structure of murine CEACAM1b -

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Basic information

Entry
Database: PDB / ID: 5vst
TitleCrystal structure of murine CEACAM1b
ComponentsBiliary glycoprotein
KeywordsCELL ADHESION / coronavirus / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of immune system process / protein tyrosine kinase binding / cell surface / signal transduction / plasma membrane
Similarity search - Function
: / 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 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
Biliary glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPeng, G. / Yang, Y. / Pasquarella, J.R. / Xu, L. / Qian, Z. / Holmes, K.V. / Li, F.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Molecular mechanism for coronavirus-driven evolution of mouse receptor
Authors: Peng, G. / Yang, Y. / Pasquarella, J.R. / Xu, L. / Qian, Z. / Holmes, K.V. / Li, F.
History
DepositionMay 12, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2017ID: 5F1D
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Biliary glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6662
Polymers23,2421
Non-polymers4241
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint6 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.097, 113.097, 64.380
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Biliary glycoprotein


Mass: 23241.986 Da / Num. of mol.: 1 / Fragment: residues 35-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ceacam1, Bgph / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q61354
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 5.11 Å3/Da / Density % sol: 75.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl, PEG4000, NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC HF-4M / Detector: PIXEL / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.098→16.969 Å / Num. obs: 8557 / % possible obs: 96.3 % / Redundancy: 2.5 % / Rsym value: 0.114 / Net I/σ(I): 9.15

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R4D

3r4d


Resolution: 3.1→16.969 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.14 / SU ML: 0.253 / Cross valid method: THROUGHOUT / ESU R: 0.637 / ESU R Free: 0.363 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25774 438 5.1 %RANDOM
Rwork0.21248 ---
obs0.21467 8119 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.829 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.47 Å20 Å2
2--0.95 Å2-0 Å2
3----3.08 Å2
Refinement stepCycle: 1 / Resolution: 3.1→16.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 28 10 1581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191600
X-RAY DIFFRACTIONr_bond_other_d0.0020.021455
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9622187
X-RAY DIFFRACTIONr_angle_other_deg0.93233394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.99525.77571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.429157
X-RAY DIFFRACTIONr_chiral_restr0.0820.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
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_it2.2245.418795
X-RAY DIFFRACTIONr_mcbond_other2.2155.416794
X-RAY DIFFRACTIONr_mcangle_it3.6768.125992
X-RAY DIFFRACTIONr_mcangle_other3.6758.128993
X-RAY DIFFRACTIONr_scbond_it2.2065.665805
X-RAY DIFFRACTIONr_scbond_other2.2055.664806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7868.3951196
X-RAY DIFFRACTIONr_long_range_B_refined6.05663.4531617
X-RAY DIFFRACTIONr_long_range_B_other6.05563.4351618
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.098→3.176 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 24 -
Rwork0.346 492 -
obs--82.17 %

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