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1fif

N-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN-A (QPDWG-HDRPY)

Method: X-RAY DIFFRACTION Dmax: 80.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

MANNOSE-BINDING PROTEIN-A

Rattus norvegicus

UniProt P19999

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 90–238 Chain B； UniProt 90–238 Chain C； UniProt 90–238 Fragment：RESIDUES 73-226 Mutation：E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y CA CALCIUM ION × 9 CL CHLORIDE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；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 Resolution 1.95 Å R-free 0.229

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1FIF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AFA STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS Deposited 1995-11-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) MBG methyl beta-D-galactopyranoside × 3 CA CALCIUM ION × 9 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.00 Å R-free 0.268
1AFB STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS Deposited 1995-11-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 3 CA CALCIUM ION × 9 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 1.90 Å R-free 0.261
1AFD STRUCTURAL BASIS OF GALACTOSE RECOGNITION IN C-TYPE ANIMAL LECTINS Deposited 1995-11-03 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT (RESIDUES 73 - 226)
Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) Mutation：E185Q, N187D, H189W, G190Y, S191G, INS(H192, G193, L194, G195, G196) CA CALCIUM ION × 8 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.0
Resolution 2.00 Å R-free 0.282
1BCH MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGH) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE Deposited 1998-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Mutation：E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Mutation：E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Mutation：E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 CA CALCIUM ION × 9 CL CHLORIDE ION × 3 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；12% PEG8000, 100MM TRIS/PH8.0, 20MM CALCIUM CHLORIDE, 10MM SODIUM CHLORIDE
Resolution 2.00 Å R-free 0.252
1BCJ MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGHV) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE Deposited 1998-04-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT RESIDUES 73 - 226
Mutation：S154V, E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Mutation：S154V, E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H Mutation：S154V, E185Q, N187D, H189W, G190Y, S191G, INS (H192, G193, L194, G195, G196), T202H NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 3 CA CALCIUM ION × 9 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；12% PEG8000, 100MM TRIS/PH8.0, 20MM CALCIUM CHLORIDE, 10MM SODIUM CHLORIDE
Resolution 2.10 Å R-free 0.261
1BUU ONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A Deposited 1998-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 71–238（168 aa） Fragment：LECTIN, TRIMERIZATION, AND PORTION OF COLLAGENOUS DOMAIN DOMAINS
Not recorded HO HOLMIUM ATOM × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIR CONTAINING 11-15% (W/V) PEG 3350, 0.325 MM HOCL3, 100 MM TRIS-CL PH 8.0, 10 MM NACL, 0.02% NAN3., vapor diffusion - hanging drop
Resolution 1.90 Å R-free 0.214
1BUU ONE HO3+ FORM OF RAT MANNOSE-BINDING PROTEIN A Deposited 1998-09-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 71–238（168 aa） Fragment：LECTIN, TRIMERIZATION, AND PORTION OF COLLAGENOUS DOMAIN DOMAINS
Not recorded HO HOLMIUM ATOM × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；HANGING-DROP VAPOR DIFFUSION AGAINST RESERVOIR CONTAINING 11-15% (W/V) PEG 3350, 0.325 MM HOCL3, 100 MM TRIS-CL PH 8.0, 10 MM NACL, 0.02% NAN3., vapor diffusion - hanging drop
Resolution 1.90 Å R-free 0.214
1FIH N-ACETYLGALACTOSAMINE BINDING MUTANT OF MANNOSE-BINDING PROTEIN A (QPDWG-HDRPY), COMPLEX WITH N-ACETYLGALACTOSAMINE Deposited 2000-08-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：RESIDUES 73-226
Chain B 90–238（149 aa） Fragment：RESIDUES 73-226
Chain C 90–238（149 aa） Fragment：RESIDUES 73-226
Mutation：E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y Mutation：E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y Mutation：E185Q, N187D, H189W, INS(Y190, G191, H192, G193, L194), S196G, T202H, I212D, A216R, S217P, H218Y NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 4 CA CALCIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；13.5% Polyethylene glycol 8000 100 mM Tris-HCL 10 mM NaCl 20 mM CaCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.95 Å R-free 0.269
1KMB SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A Deposited 1996-11-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K CA CALCIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；8-10% PEG 8000, 2% PEG 1000, 1 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTION, THE CRYSTAL WAS ADAPTED TO THE MOTHER LIQUOR PLUS 20% MPD.
Resolution 2.10 Å R-free 0.265
1KWT Rat mannose binding protein A (native, MPD) Deposited 2002-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.95 Å R-free 0.234
1KWU Rat mannose binding protein A complexed with a-Me-Man Deposited 2002-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded MMA methyl alpha-D-mannopyranoside × 3 CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.95 Å R-free 0.241
1KWV Rat mannose binding protein A complexed with a-Me-GlcNAc Deposited 2002-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.249
1KWW Rat mannose protein A complexed with a-Me-Fuc. Deposited 2002-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded MFU methyl alpha-L-fucopyranoside × 3 CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.90 Å R-free 0.224
1KWX Rat mannose protein A complexed with b-Me-Fuc. Deposited 2002-01-30 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded MFB methyl beta-L-fucopyranoside × 3 CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2, 200mM b-Me-Fuc. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.229
1KWY Rat mannose protein A complexed with man-a13-man. Deposited 2002-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2, 200mM man-a13-man. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.231
1KWZ Rat mannose protein A (H189V) complexed with Man-a13-Man Deposited 2002-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Mutation：H189V Mutation：H189V Mutation：H189V CA CALCIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2, 200mM man-a13-man. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 1.90 Å R-free 0.252
1KX0 Rat mannose protein A (H189V I207V) complexed with man-a13-man Deposited 2002-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Mutation：H189V, I207V Mutation：H189V, I207V Mutation：H189V, I207V CA CALCIUM ION × 9 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；8-13% PEG 8000 or 3500, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 12mg/ml in 10 mM NaCl, 10mM CaCl2, 200mM man-a13-man. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.00 Å R-free 0.232
1KX1 Rat mannose protein A complexed with Man6-GlcNAc2-Asn Deposited 2002-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain B 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain C 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded CA CALCIUM ION × 9 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；10% PEG 8000, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 5mg/ml in 10mM Tris-Cl pH=8.0, 10 mM NaCl, 20mM CaCl2, 1.1mM Man6GlcNAc2Asn. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.80 Å R-free 0.287
1KX1 Rat mannose protein A complexed with Man6-GlcNAc2-Asn Deposited 2002-01-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain E 90–238（149 aa） Fragment：residues 90-238 of P19999
Chain F 90–238（149 aa） Fragment：residues 90-238 of P19999
Not recorded CA CALCIUM ION × 9 MAN alpha-D-mannopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；10% PEG 8000, 100mM Tris-Cl pH=8.0, 10mM NaCl, 20mM Cacl2, 2mM NaN3. Protein solution: 5mg/ml in 10mM Tris-Cl pH=8.0, 10 mM NaCl, 20mM CaCl2, 1.1mM Man6GlcNAc2Asn. VAPOR DIFFUSION, HANGING DROP at 298K
Resolution 2.80 Å R-free 0.287
1MSB STRUCTURE OF THE CALCIUM-DEPENDENT LECTIN DOMAIN FROM A RAT MANNOSE-BINDING PROTEIN DETERMINED BY MAD PHASING Deposited 1991-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 124–238（115 aa）
Chain B 124–238（115 aa）
Not recorded HO HOLMIUM ATOM × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1RTM TRIMERIC STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN Deposited 1994-11-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa）
Chain 2 90–238（149 aa）
Chain 3 90–238（149 aa）
Not recorded CA CALCIUM ION × 9 CL CHLORIDE ION × 3 GOL GLYCEROL × 15 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.270
1YTT YB SUBSTITUTED SUBTILISIN FRAGMENT OF MANNOSE BINDING PROTEIN-A (SUB-MBP-A), MAD STRUCTURE AT 110K Deposited 1995-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 124–238（115 aa） Fragment：SUBTILISIN FRAGMENT RESIDUES 107 - 221
Chain B 124–238（115 aa） Fragment：SUBTILISIN FRAGMENT RESIDUES 107 - 221
Not recorded YB YTTERBIUM (III) ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.80 Å R-free 0.206
2KMB COMPLEX OF 3'-NEUAC-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A Deposited 1996-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K CA CALCIUM ION × 10 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；8-10% PEG 8000, 2% PEG 1000, 1 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTION, THE CRYSTAL WAS ADAPTED TO THE MOTHER LIQUOR PLUS 20% MPD PLUS 80 MM 3'-NEUAC-LEWIS-X.
Resolution 2.00 Å R-free 0.247
2MSB STRUCTURE OF A C-TYPE MANNOSE-BINDING PROTEIN COMPLEXED WITH AN OLIGOSACCHARIDE Deposited 1992-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 124–238（115 aa）
Chain B 124–238（115 aa）
Not recorded CA CALCIUM ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.70 Å
3KMB COMPLEX OF 3'-SULFO-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A Deposited 1996-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K CA CALCIUM ION × 10 CL CHLORIDE ION × 3 FUC alpha-L-fucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED FROM 8-10% PEG 8000, 2% PEG 1000, 100 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTED, THE CRYSTAL WAS SOAKED IN THE MOTHER LIQUOR MINUS PEG 8000, PLUS 35% PEG 400, PLUS 80 MM 3'-SULFO- LEWIS-X.
Resolution 1.95 Å R-free 0.254
4KMB COMPLEX OF 4'-SULFO-LEWIS-X WITH A SELECTIN-LIKE MUTANT OF MANNOSE-BINDING PROTEIN A Deposited 1996-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 3 PDB declaration: trimeric
Chain 1 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 2 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Chain 3 90–238（149 aa） Fragment：CLOSTRIPAIN FRAGMENT
Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K Mutation：A211K, S212K, H213K CA CALCIUM ION × 11 CL CHLORIDE ION × 3 ZN ZINC ION × 1 FUC alpha-L-fucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED FROM 8-10% PEG 8000, 2% PEG 1000, 100 MM TRIS-CL, PH 7.8, 200 MM NACL, 20 MM CACL2, 2 MM NAN3. PRIOR TO DATA COLLECTION, THE CRYSTAL WAS ADAPTED TO THE MOTHER LIQUOR MINUS PEG 8000, PLUS 35% PEG 400, PLUS 80 MM 4'-SULFO- LEWIS-X.
Resolution 2.00 Å R-free 0.272

24 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MBL1_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–154； UniProt 90–238 Author chain B； PDBConstruct 1–154； UniProt 90–238 Author chain C； PDBConstruct 1–154； UniProt 90–238

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1fif

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1fif
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1fif
Deposition date deposition_date2000-08-03
Structure title titleN-ACETYLGALACTOSAMINE-SELECTIVE MUTANT OF MANNOSE-BINDING PROTEIN-A (QPDWG-HDRPY)
Keywords keywordsLECTIN, C-TYPE LECTIN, CALCIUM-BINDING PROTEIN, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.41 Å
Radius of gyration Rg (electron density) rg_electron26.48 Å
Forward intensity I(0) i046547400.00
Molecular weight molecular_weight51913.0 kDa
Excluded volume excluded_volume64524 ų
Envelope volume envelope_volume79110 ų
Hydration-shell volume shell_volume26120 ų
Envelope diameter envelope_diameter83.5 Å
Shell Rg shell_rg32.30 Å
Envelope Rg envelope_rg26.60 Å
Shape Rg shape_rg26.47 Å
Total Rg total_rg27.16 Å
Total atoms total_atoms3626
Residues n_residues462
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax80.3 Å
Rg (real space) rg_real27.28 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real4.6550e+07
I(0) uncertainty (real space) i0_real_error5.7570e+05
Rg (reciprocal space) rg_reciprocal27.33 Å
I(0) (reciprocal space) i0_reciprocal46550000.0000
Solution quality estimate total_estimate0.9136
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.1 Å
Skewness Skewness skewness0.040
Kurtosis Kurtosis kurtosis-0.782
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8962000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.980; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.939
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1fifa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd1fifa2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins
Domain ID domain_idd1fifb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd1fifb2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins
Domain ID domain_idd1fifc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.169 — C-type lectin-like
Superfamily Superfamily superfamilyd.169.1 — C-type lectin-like
Family Family familyd.169.1.1 — C-type lectin domain
Domain ID domain_idd1fifc2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.1 — Triple coiled coil domain of C-type lectins
Family Family familyh.1.1.1 — Triple coiled coil domain of C-type lectins

CATH v4.4 (3 domains)

Domain ID domain_id1fifA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id1fifB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
Domain ID domain_id1fifC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily10 — Mannose-Binding Protein A, subunit A
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8. Citations (1)

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9. Files and Curves (10)