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- PDB-1ytt: YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (... -

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Basic information

Entry
Database: PDB / ID: 1ytt
TitleYB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K
ComponentsMANNOSE-BINDING PROTEIN A
KeywordsMANNOSE-BINDING PROTEIN / CARBOHYDRATE / RECOGNITION DOMAIN / CALCIUM DEPENDENT
Function / homology
Function and homology information


calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / protein homotrimerization / D-mannose binding / polysaccharide binding ...calcium-dependent carbohydrate binding / complement activation, lectin pathway / oligosaccharide binding / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / phosphatidylinositol-4-phosphate binding / protein homotrimerization / D-mannose binding / polysaccharide binding / complement activation, classical pathway / multivesicular body / positive regulation of phagocytosis / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / calcium ion binding / protein homodimerization activity / 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
YTTERBIUM (III) ION / Mannose-binding protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsBurling, F.T. / Weis, W.I. / Flaherty, K.M. / Brunger, A.T.
Citation
Journal: Science / Year: 1996
Title: Direct observation of protein solvation and discrete disorder with experimental crystallographic phases.
Authors: Burling, F.T. / Weis, W.I. / Flaherty, K.M. / Brunger, A.T.
#1: 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. / Hendrickson, W.A. / Drickamer, K.
#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.
History
DepositionNov 9, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MANNOSE-BINDING PROTEIN A
B: MANNOSE-BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0686
Polymers25,3762
Non-polymers6924
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.508, 72.216, 45.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12688.150 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT RESIDUES 107 - 221
Source method: isolated from a genetically manipulated source
Details: MAD DATA TAKEN ON FROZEN CRYSTAL (110K) / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P19999
#2: Chemical
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Yb
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CYS 128 - CYS 217 DISULFIDE IS PARTIALLY REDUCED.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal grow
*PLUS
pH: 8 / Method: unknown
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mg/mlprotein1drop
210 mM1dropCaCl2
35 mM1dropNaCl
41.1 mM1dropMan6GlcNAc2Asn
515-20 %PEG33501reservoiror PEG8000
620 mM1reservoirCaCl2
7100 mMTris-HCl1reservoir
810 mM1reservoirNaCl
90.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.3565, 1.3849, 1.3854, 1.3860
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Sep 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.35651
21.38491
31.38541
41.3861
ReflectionRedundancy: 0.036 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.077
Reflection
*PLUS
Rmerge(I) obs: 0.077

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Processing

Software
NameVersionClassification
DENZO-SCALEPACKdata collection
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementResolution: 1.8→10 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.206 --
Rwork0.185 --
obs0.185 36619 96.3 %
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.71 Å20 Å20 Å2
2---2.23 Å20 Å2
3----1.48 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: -0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1765 0 4 158 1927
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1TOPPAR:PARHCSDX.PRO
X-RAY DIFFRACTION2TOPPAR:PARAM19.SOL
X-RAY DIFFRACTION3YBPARAM.YB
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_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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