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- PDB-6ryj: structure of conglutinin carbohydrate recognition domain with eth... -

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Basic information

Entry
Database: PDB / ID: 6ryj
Titlestructure of conglutinin carbohydrate recognition domain with ethylene glycol bound
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 / molecular replacement / Resolution: 1.25 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)14,2254
Polymers14,0831
Non-polymers1423
Water1,820101
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 area390 Å2
ΔGint-22 kcal/mol
Surface area6630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.822, 50.822, 52.837
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.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.42 Å3/Da / Density % sol: 49.23 % / Mosaicity: 0.3 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / 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: SRS / Beamline: PX14.2 / Wavelength: 0.985 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.985 Å / Relative weight: 1
ReflectionResolution: 1.25→52.868 Å / Num. obs: 35164 / % possible obs: 94.3 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.039 / Rsym value: 0.034 / Net I/av σ(I): 12.3 / Net I/σ(I): 27.5 / Num. measured all: 348475
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allRsym value% possible all
1.25-1.294.30.1993.523670.2690.19966.9
1.29-1.385.50.1584.651810.2050.15885.7
1.38-1.498.40.1136.756250.1360.11398.9
1.49-1.639.20.06810.752100.0810.068100
1.63-1.839.30.04415.547390.0530.04499.9
1.83-2.1111.10.04114.441790.0470.041100
2.11-2.5816.30.0381735390.0420.038100
2.58-3.6616.40.0320.127710.0330.03100
3.66-52.86813.50.02721.115530.030.027100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.4data scaling
AMoREphasing
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1pw9

1pw9


Resolution: 1.25→50.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.616 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0446 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1738 4.9 %RANDOM
Rwork0.181 ---
obs0.182 33397 94.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 58.5 Å2 / Biso mean: 15.101 Å2 / Biso min: 6.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---0.22 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.25→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 6 101 1047
Biso mean--21.67 24.14 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.013969
X-RAY DIFFRACTIONr_bond_other_d0.0010.018843
X-RAY DIFFRACTIONr_angle_refined_deg1.6821.6481313
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5781980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25525.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.87215161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.923154
X-RAY DIFFRACTIONr_chiral_restr0.0710.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021119
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 82 -
Rwork0.229 1701 -
all-1783 -
obs--64.84 %

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