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- PDB-1bch: MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL... -

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Basic information

Entry
Database: PDB / ID: 1bch
TitleMANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE
ComponentsMANNOSE-BINDING PROTEIN-A
KeywordsLECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN
Function / homologyC-type lectin domain profile. / C-type lectin domain signature. / Collagen triple helix repeat (20 copies) / Lectin C-type domain / Mannose-binding protein / Collectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin fold / C-type lectin-like/link domain superfamily / Collagen triple helix repeat ...C-type lectin domain profile. / C-type lectin domain signature. / Collagen triple helix repeat (20 copies) / Lectin C-type domain / Mannose-binding protein / Collectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin fold / C-type lectin-like/link domain superfamily / Collagen triple helix repeat / C-type lectin-like / calcium-dependent carbohydrate binding / growth plate cartilage chondrocyte morphogenesis / killing by host of symbiont cells / complement activation, lectin pathway / oligosaccharide binding / phosphatidylinositol-4-phosphate binding / negative regulation of growth of symbiont in host / collagen trimer / polysaccharide binding / mannose binding / positive regulation of phagocytosis / protein homotrimerization / extracellular matrix / calcium-dependent protein binding / complement activation, classical pathway / protein homotetramerization / protease binding / defense response to Gram-positive bacterium / calcium ion binding / protein homodimerization activity / extracellular space / Mannose-binding protein A
Function and homology information
Specimen sourceRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2 Å resolution
AuthorsKolatkar, A.R. / Weis, W.I.
Citation
Journal: J.Biol.Chem. / Year: 1998
Title: Mechanism of N-acetylgalactosamine binding to a C-type animal lectin carbohydrate-recognition domain.
Authors: Kolatkar, A.R. / Leung, A.K. / Isecke, R. / Brossmer, R. / Drickamer, K. / Weis, W.I.
#1: Journal: J.Biol.Chem. / Year: 1996
Title: Selective Sugar Binding to the Carbohydrate Recognition Domains of the Rat Hepatic and Macrophage Asialoglycoprotein Receptors
Authors: Iobst, S.T. / Drickamer, K.
#2: Journal: J.Biol.Chem. / Year: 1996
Title: Structural Basis of Galactose Recognition by C-Type Animal Lectins
Authors: Kolatkar, A.R. / Weis, W.I.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 30, 1998 / Release: Jun 17, 1998
RevisionDateData content typeGroupProviderType
1.0Jun 17, 1998Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: MANNOSE-BINDING PROTEIN-A
2: MANNOSE-BINDING PROTEIN-A
3: MANNOSE-BINDING PROTEIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,34119
Polyers51,1873
Non-polymers1,15416
Water5,873326
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)8170
ΔGint (kcal/M)-166
Surface area (Å2)22320
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)80.490, 85.010, 98.710
Angle α, β, γ (deg.)90.00, 104.82, 90.00
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 1 types, 3 molecules 123

#1: Protein/peptide MANNOSE-BINDING PROTEIN-A / CL-QPDWGH


Mass: 17062.338 Da / Num. of mol.: 3 / Fragment: CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Mutation: E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Genus: Rattus
Description: THE BACTERIALLY EXPRESSED MATERIAL WAS DIGESTED WITH CLOSTRIPAIN TO PRODUCE THE PROTEIN USED IN THE CRYSTAL STRUCTURE ANALYSIS
Plasmid name: PINIIIOMPA2 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P19999

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Non-polymers , 6 types, 342 molecules

#2: Chemical ChemComp-A2G / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Mass: 221.208 Da / Num. of mol.: 1 / Formula: C8H15NO6
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Formula: Ca / Calcium
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Formula: Cl / Chloride
#5: Chemical ChemComp-NGA / N-ACETYL-D-GALACTOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylgalactosamine
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Formula: Na / Sodium
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Formula: H2O / Water

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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: 3.2 / Density percent sol: 60.9 %
Description: 20% 2-METHYL,2-4 PENTANEDIOL (CRYOPROTECTANT), 200MM N-ACETYL-D-GALACTOSAMINE
Crystal growpH: 8
Details: 12% PEG8000, 100MM TRIS/PH8.0, 20MM CALCIUM CHLORIDE, 10MM SODIUM CHLORIDE
Crystal grow
*PLUS
Temp: 20 ℃ / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
110-20 mg/mlprotein1drop
210 mM1dropNaCl
310 mM1dropCaCl2
412-15 %PEG80001reservoir
5100 mMTris-HCl1reservoir
620 mM1reservoirCaCl2
70.02 %1reservoirNaN3
8200 mMGalNAc1drop
9MPD1drop

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Collection date: Sep 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 20.1 Å2 / D resolution high: 2 Å / D resolution low: 3 Å / Number obs: 42942 / Observed criterion sigma I: -3 / Rmerge I obs: 0.042 / Rsym value: 0.042 / NetI over sigmaI: 11.7 / Redundancy: 2.8 % / Percent possible obs: 98.5
Reflection shellRmerge I obs: 0.272 / Highest resolution: 2 Å / Lowest resolution: 2.09 Å / MeanI over sigI obs: 4.8 / Rsym value: 0.272 / Redundancy: 2.7 % / Percent possible all: 97
Reflection shell
*PLUS
Percent possible obs: 97

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFB
R Free selection details: RANDOM / Data cutoff high absF: 2657.155 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES
Solvent computationSolvent model details: FLAT MODEL / Solvent model param bsol: 37.7 / Solvent model param ksol: 0.33
Displacement parametersB iso mean: 36.9 Å2 / Aniso B11: -2.5 Å2 / Aniso B12: 0 Å2 / Aniso B13: -7.12 Å2 / Aniso B22: 5.3 Å2 / Aniso B23: 0 Å2 / Aniso B33: -2.8 Å2
Least-squares processR factor R free: 0.252 / R factor R free error: 0.004 / R factor R work: 0.219 / R factor obs: 0.219 / Highest resolution: 2 Å / Lowest resolution: 3 Å / Number reflection R free: 4310 / Number reflection obs: 42001 / Percent reflection R free: 10.3 / Percent reflection obs: 96.4
Refine analyzeLuzzati coordinate error free: 0.31 Å / Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.23 Å / Luzzati sigma a obs: 0.17 Å
Refine hist #LASTHighest resolution: 2 Å / Lowest resolution: 3 Å
Number of atoms included #LASTProtein: 3588 / Nucleic acid: 0 / Ligand: 60 / Solvent: 326 / Total: 3974
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.80
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.50
X-RAY DIFFRACTIONc_mcangle_it2.162.0
X-RAY DIFFRACTIONc_scbond_it2.212.0
X-RAY DIFFRACTIONc_scangle_it3.322.50
Refine LS shellHighest resolution: 2 Å / R factor R free: 0.324 / R factor R free error: 0.014 / R factor R work: 0.273 / Lowest resolution: 2.09 Å / Number reflection R free: 520 / Number reflection R work: 4397 / Total number of bins used: 8 / Percent reflection R free: 10.6 / Percent reflection obs: 90.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMTOPH.CHO
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3C / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.80
Refine LS shell
*PLUS
R factor obs: 0.273

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