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Yorodumi- PDB-1igf: CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1igf | ||||||
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Title | CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS | ||||||
Components |
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Keywords | IMMUNOGLOBULIN | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Stanfield, R.L. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 1990 Title: Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. Authors: Stanfield, R.L. / Fieser, T.M. / Lerner, R.A. / Wilson, I.A. #1: Journal: J.Biol.Chem. / Year: 1989 Title: Preliminary Crystallographic Data and Primary Sequence for Anti-Peptide Fab' B13I2 and its Complex with the C-Helix Peptide from Myohemerythrin Authors: Stura, E.A. / Stanfield, R.L. / Fieser, T.M. / Balderas, R.S. / Smith, L.R. / Lerner, R.A. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1igf.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1igf.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 1igf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1igf_validation.pdf.gz | 422.5 KB | Display | wwPDB validaton report |
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Full document | 1igf_full_validation.pdf.gz | 461.4 KB | Display | |
Data in XML | 1igf_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 1igf_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/1igf ftp://data.pdbj.org/pub/pdb/validation_reports/ig/1igf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 8, 95, AND 141 OF THE *L* AND *M* CHAINS AND RESIDUES 149 AND 151 OF THE *H* AND *J* CHAINS ARE CIS PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.246, 0.12614, -0.96103), Vector: Details | THE TWO FAB' HEAVY CHAINS (RESIDUES 1-227) OF THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN INDICATORS *H* AND *J*. THERE ARE TWO FAB MOLECULES PER ASYMMETRIC UNIT. THE NON-CRYSTALLOGRAPHIC TRANSFORMATION PRESENTED ON THE *MTRIX* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR MOLECULE 2 WHEN APPLIED TO MOLECULE 1 (COORDINATES OF CHAIN *M* FROM CHAIN *L* AND COORDINATES OF CHAIN *J* FROM CHAIN *H*). | |
-Components
#1: Antibody | Mass: 24148.803 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: PC4203 #2: Antibody | Mass: 23807.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38864 #3: Sugar | ChemComp-NAG / | Nonpolymer details | NAG N 901 IS LINKED TO ASN L 26 OF THE FIRST FAB' FRAGMENT IN THE ASYMMETRIC UNIT. BECAUSE DENSITY ...NAG N 901 IS LINKED TO ASN L 26 OF THE FIRST FAB' FRAGMENT IN THE ASYMMETRIC | Sequence details | THE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M. ...THE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.69 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, sitting dropDetails: taken from Stura, E.A. et al(1989). J. Biol. Chem., 264, 15721-15725. | ||||||||||||||||||||
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 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.8→8 Å / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.71 |