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Yorodumi- PDB-1mco: THREE-DIMENSIONAL STRUCTURE OF A HUMAN IMMUNOGLOBULIN WITH A HING... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mco | |||||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF A HUMAN IMMUNOGLOBULIN WITH A HINGE DELETION | |||||||||
Components |
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Keywords | IMMUNOGLOBULIN | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | |||||||||
Authors | Guddat, L.W. / Edmundson, A.B. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 1993 Title: Three-dimensional structure of a human immunoglobulin with a hinge deletion. Authors: Guddat, L.W. / Herron, J.N. / Edmundson, A.B. #1: Journal: Mol.Immunol. / Year: 1983 Title: Three-Dimensional Structure of the Mcg Igg1 Immunoglobulin Authors: Rajan, S.S. / Ely, K.R. / Abola, E.E. / Wood, M.K. / Colman, P.M. / Athay, R.J. / Edmundson, A.B. #2: Journal: Contemp.Top.Mol.Immunol. / Year: 1978 Title: Conformational Flexibility in Immunoglobulins Authors: Edmundson, A.B. / Ely, K.R. / Abola, E.E. #3: Journal: J.Biol.Chem. / Year: 1970 Title: A Crystallographic Investigation of a Human Igg Immunoglobulin Authors: Edmundson, A.B. / Wood, M.K. / Schiffer, M. / Hardman, K.D. / Ainsworth, C.F. / Ely, K.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mco.cif.gz | 126.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mco.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mco.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mco_validation.pdf.gz | 499.3 KB | Display | wwPDB validaton report |
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Full document | 1mco_full_validation.pdf.gz | 572.1 KB | Display | |
Data in XML | 1mco_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1mco_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mc/1mco ftp://data.pdbj.org/pub/pdb/validation_reports/mc/1mco | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: TYR L 144 - PRO L 145 OMEGA ANGLE = 90.421 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: PHE H 150 - PRO H 151 OMEGA ANGLE = 235.747 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: GLN H 152 - PRO H 153 OMEGA ANGLE = 247.018 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: TYR H 358 - PRO H 359 OMEGA ANGLE = 278.722 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 5: PRO H 380 - PRO H 381 OMEGA ANGLE = 221.018 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Antibody | Mass: 22835.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: PIR: S14675 |
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#2: Antibody | Mass: 46898.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 243866 |
#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-gulopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
Sequence details | THE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM OF ...THE FOLLOWING TABLE MAY BE USED TO RELATE THE ENTRIES SEQUENCE NUMBERING TO THE NUMBERING SYSTEM OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY,K.S.GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.18 % | ||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: unknown / Details: Edmundson, A.B., (1970) J.Biol.Chem., 245, 2763. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 9999 Å / Num. all: 15365 / Num. obs: 14525 / % possible obs: 94.5 % / Num. measured all: 43520 / Rmerge(I) obs: 0.1479 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.232 / Rfactor obs: 0.232 / Highest resolution: 3.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.2 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 3.2 Å / Rfactor obs: 0.232 / Lowest resolution: 6 Å / Num. reflection obs: 11875 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 0.027 |