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- PDB-1kzb: Complex of MBP-C and trimannosyl core -

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Basic information

Entry
Database: PDB / ID: 1kzb
TitleComplex of MBP-C and trimannosyl core
ComponentsMANNOSE-BINDING PROTEIN C
KeywordsIMMUNE SYSTEM / SUGAR BINDING PROTEIN / protein-carbohydrate complex
Function / homology
Function and homology information


Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / complement activation, lectin pathway / positive regulation of complement activation / negative regulation of viral process / galactose binding / killing by host of symbiont cells / positive regulation of protein processing / cell surface pattern recognition receptor signaling pathway ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / complement activation, lectin pathway / positive regulation of complement activation / negative regulation of viral process / galactose binding / killing by host of symbiont cells / positive regulation of protein processing / cell surface pattern recognition receptor signaling pathway / collagen trimer / serine-type endopeptidase complex / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / D-mannose binding / complement activation, classical pathway / multivesicular body / antiviral innate immune response / positive regulation of phagocytosis / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / signaling receptor binding / innate immune response / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding
Similarity search - Function
Collectin, C-type lectin-like domain / : / 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. ...Collectin, C-type lectin-like domain / : / 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
alpha-D-mannopyranose / Mannose-binding protein C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsNg, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition.
Authors: Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: MANNOSE-BINDING PROTEIN C
2: MANNOSE-BINDING PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1818
Polymers25,6612
Non-polymers5216
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-58 kcal/mol
Surface area10980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.720, 75.330, 57.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Detailsnon-physiological dimer

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Components

#1: Protein MANNOSE-BINDING PROTEIN C / MBP-C / MANNAN-BINDING PROTEIN / RA-REACTIVE FACTOR P28A SUBUNIT / RARF/P28A


Mass: 12830.325 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: MBL1 / Plasmid: pINOmpIIIA2 / Production host: Escherichia coli (E. coli) / Strain (production host): JA221 / References: UniProt: P08661
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112-20 mg/mlprotein1drop
210 mMTris-Cl1droppH7.5
312 mM1dropCaCl2
411-14 %PEG80001reservoir
5100 mMTris-Cl1reservoirpH7.4
6100 mM1reservoirNaCl
712 mM1reservoirCaCl2
82 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 10, 1994
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 23828 / Num. obs: 23828 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 17.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.111 / Mean I/σ(I) obs: 4 / Num. unique all: 2006 / Rsym value: 0.111 / % possible all: 81.8
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Redundancy: 3.5 %
Reflection shell
*PLUS
% possible obs: 81.8 % / Redundancy: 1.8 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1RDO

1rdo


Resolution: 1.8→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2179 10.1 %random
Rwork0.212 ---
all0.217 21681 --
obs0.217 21681 86.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.019 Å20 Å20 Å2
2---1.989 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 28 293 2049
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_d1.3
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_d

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