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- PDB-1rdi: MANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1rdi
TitleMANNOSE-BINDING PROTEIN, SUBTILISIN DIGEST FRAGMENT COMPLEX WITH ALPHA-METHYL-L-FUCOPYRANOSIDE
ComponentsMANNOSE-BINDING PROTEIN-C
KeywordsLECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN
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
methyl alpha-L-fucopyranoside / Mannose-binding protein C
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsNg, K.K.-S. / Drickamer, K. / Weis, W.I.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Structural analysis of monosaccharide recognition by rat liver mannose-binding protein.
Authors: Ng, K.K. / Drickamer, K. / Weis, W.I.
#1: Journal: Nature / Year: 1992
Title: Structure of a C-Type Mannose-Binding Protein Complexed with an Oligosaccharide
Authors: Weis, W.I. / Drickamer, K. / Hendrickson, W.A.
#2: Journal: Science / Year: 1991
Title: Structure of the Calcium-Dependent Lectin Domain from a Rat Mannose-Binding Protein Determined by MAD Phasing
Authors: Weis, W.I. / Kahn, R. / Fourme, R. / Drickamer, K. / Hendrickson, W.A.
#3: Journal: J.Biol.Chem. / Year: 1991
Title: Physical Characterization and Crystallization of the Carbohydrate-Recognition Domain of a Mannose-Binding Protein from Rat
Authors: Weis, W.I. / Crichlow, G.V. / Murthy, H.M.K. / Hendrickson, W.A. / Drickamer, K.
#4: Journal: J.Biol.Chem. / Year: 1990
Title: Differential Recognition of Core and Terminal Portions of Oligosaccharide Ligands by Carbohydrate-Recognition Domains of Two Mannose-Binding Proteins
Authors: Childs, R.A. / Feizi, T. / Yuen, C.-T. / Drickamer, K. / Quesenberry, M.S.
History
DepositionSep 5, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 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.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _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 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)25,9029
Polymers25,3502
Non-polymers5527
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-67 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.700, 75.100, 57.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 1 191 / 2: CIS PROLINE - PRO 2 191
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999787, 0.016877, 0.011914), (0.017113, -0.999654, -0.019969), (0.011573, 0.020168, -0.99973)
Vector: -0.3965, 37.4619, 6.327)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 1 115 .. 1 225 2 115 .. 2 225 0.267

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Components

#1: Protein MANNOSE-BINDING PROTEIN-C / SUB-MBP-C


Mass: 12675.127 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT (RESIDUES 114 - 226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat)
Description: THE BACTERIALLY EXPRESSED MATERIAL IS DIGESTED WITH SUBTILISIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS
Organ: LIVER / Plasmid: PINIIIOMPA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P08661
#2: Sugar ChemComp-MFU / methyl alpha-L-fucopyranoside / ALPHA-L-METHYL-FUCOSE / methyl 6-deoxy-alpha-L-galactopyranoside / methyl alpha-L-fucoside / methyl L-fucoside / methyl fucoside


Type: L-saccharide / Mass: 178.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H14O5
IdentifierTypeProgram
LFucp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-L-fucopyranoseCOMMON NAMEGMML 1.0
o1-methyl-a-L-fucoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growpH: 7.4 / Details: pH 7.4, 20% MPD USED AS A CRYOPROTECTANT
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112-20 mg/mlprotein1drop
2110 mMTris-HCl1drop
324 mM1dropCaCl2
411-14 %(w/v)PEG80001drop
5100 mM1dropNaCl
62 mM1dropNaN3
711-14 %(w/v)PEG80001reservoir
8100 mMTris-HCl1reservoir
9100 mM1reservoirNaCl
102 mM1reservoirNaN3
1112 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 8, 1995
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 24379 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 1.8→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.244 -10 %
Rwork0.196 --
obs0.196 20202 97.8 %
Displacement parametersBiso mean: 20.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 29 284 2075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11.5
X-RAY DIFFRACTIONx_mcangle_it1.22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.42.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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