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- PDB-6ryg: native structure of conglutinin carbohydrate recognition domain -

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Basic information

Entry
Database: PDB / ID: 6ryg
Titlenative structure of conglutinin carbohydrate recognition domain
ComponentsConglutinin
KeywordsIMMUNE SYSTEM / carbohydrate recognition domain / lectin / collectin / sugar binding protein
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / collagen trimer / D-mannose binding / extracellular matrix organization / collagen-containing extracellular matrix / extracellular space
Similarity search - Function
Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. ...Lung surfactant protein D coiled-coil trimerisation / Lung surfactant protein D coiled-coil trimerisation / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.974 Å
AuthorsShrive, A.K. / Greenhough, T.J.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Atomic-resolution crystal structures of the immune protein conglutinin from cow reveal specific interactions of its binding site withN-acetylglucosamine.
Authors: Paterson, J.M. / Shaw, A.J. / Burns, I. / Dodds, A.W. / Prasad, A. / Reid, K.B. / Greenhough, T.J. / Shrive, A.K.
History
DepositionJun 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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
Item: _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: Conglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1232
Polymers14,0831
Non-polymers401
Water2,540141
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: From known literature, active molecule is composed of four trimeric units - trimeric unit is composed of N-terminal domain, collagen-like helix, alpha-helical coiled-coil and 3 carbohydrate ...Evidence: From known literature, active molecule is composed of four trimeric units - trimeric unit is composed of N-terminal domain, collagen-like helix, alpha-helical coiled-coil and 3 carbohydrate recognition domains. As the structure only contains a carbohydrate recognition domain, it is only a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.170, 50.170, 52.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Conglutinin


Mass: 14082.562 Da / Num. of mol.: 1 / Fragment: carbohydrate recognition domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CGN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23805
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.31 % / Mosaicity: 0.15 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2.5 M ammonium sulfate, 0.1 M tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 0.974→50.17 Å / Num. obs: 61295 / % possible obs: 81.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.059 / Rsym value: 0.05 / Net I/av σ(I): 7 / Net I/σ(I): 22.9 / Num. measured all: 471902
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allRsym valueNet I/σ(I) obs% possible all
0.97-1.022.30.2163.2428918880.3150.2162.320.5
1.02-1.083.40.1235.72033159260.1660.1235.255.7
1.08-1.1550.0956.64100681230.1210.09510.581.3
1.15-1.257.10.0787.46678593520.0970.07816.899.6
1.25-1.377.40.069.46320285800.0740.0621.6100
1.37-1.537.70.0579.66038578100.0690.05725.9100
1.53-1.7610.10.05410.66912668740.0620.05432.6100
1.76-2.1612.80.05110.97454858410.060.05141.8100
2.16-3.0511.90.04712.45397345270.0550.04742100
3.05-52.2477.70.04512.61825723740.0590.0453393.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.1.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RYM

6rym


Resolution: 0.974→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.461 / SU ML: 0.011 / SU R Cruickshank DPI: 0.0209 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.02
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1388 3086 5 %RANDOM
Rwork0.1347 ---
obs0.1349 58175 81.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.39 Å2 / Biso mean: 14.148 Å2 / Biso min: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 0.974→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms896 0 1 141 1038
Biso mean--16.95 25.55 -
Num. residues----116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013921
X-RAY DIFFRACTIONr_bond_other_d0.0010.018812
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.6481248
X-RAY DIFFRACTIONr_angle_other_deg1.5681.5781904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.375116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74124.69449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60915154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.245154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2119
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02179
X-RAY DIFFRACTIONr_rigid_bond_restr7.73331733
LS refinement shellResolution: 0.974→1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.461 35 -
Rwork0.498 667 -
all-702 -
obs--12.62 %

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