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- PDB-1fif: N-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN... -

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Basic information

Entry
Database: PDB / ID: 1fif
TitleN-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN-A (QPDWG-HDRPY)
ComponentsMANNOSE-BINDING PROTEIN-A
KeywordsSUGAR BINDING PROTEIN / LECTIN / C-TYPE LECTIN / CALCIUM-BINDING PROTEIN
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
Mannose-binding protein A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsFeinberg, H. / Torgersen, D. / Drickamer, K. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Mechanism of pH-dependent N-acetylgalactosamine binding by a functional mimic of the hepatocyte asialoglycoprotein receptor.
Authors: Feinberg, H. / Torgersen, D. / Drickamer, K. / Weis, W.I.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
C: MANNOSE-BINDING PROTEIN-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98814
Polymers51,5563
Non-polymers43211
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-163 kcal/mol
Surface area22840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.340, 84.833, 97.142
Angle α, β, γ (deg.)90.00, 107.88, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a trimer. The complete trimer is contained in the asymmetric unit

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Components

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


Mass: 17185.447 Da / Num. of mol.: 3 / Fragment: RESIDUES 73-226
Mutation: E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PINIIIOMPA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P19999
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 13.5% golyethylene glycol 8,000, 100 mM Tris-HCl, 10 mM NaCl, 20 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-22.5 mg/mlprotein1drop
210 mM1dropNaCl
313.5 %PEG80001reservoir
4100 mMTris-HCl1reservoir
510 mM1reservoirNaCl
620 mM1reservoirCaCl2
710 mM1dropCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 18, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→100 Å / Num. all: 120159 / Num. obs: 42884 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.9
Reflection shellResolution: 1.95→2.12 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.157 / Num. unique all: 4207 / % possible all: 93
Reflection
*PLUS
Num. measured all: 120159
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 1.95→28.68 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1848493.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3455 8.2 %RANDOM
Rwork0.193 ---
obs0.193 41932 92.5 %-
all-45246 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.46 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å22.3 Å2
2---2.35 Å20 Å2
3---2.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3629 0 11 414 4054
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.482
X-RAY DIFFRACTIONc_scangle_it3.662.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 529 8 %
Rwork0.221 6060 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / % reflection Rfree: 8 % / Rfactor Rwork: 0.221

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