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Yorodumi- PDB-1mel: CRYSTAL STRUCTURE OF A CAMEL SINGLE-DOMAIN VH ANTIBODY FRAGMENT I... -
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-Basic information
Entry | Database: PDB / ID: 1mel | ||||||
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Title | CRYSTAL STRUCTURE OF A CAMEL SINGLE-DOMAIN VH ANTIBODY FRAGMENT IN COMPLEX WITH LYSOZYME | ||||||
Components |
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Keywords | COMPLEX (ANTIBODY/ANTIGEN) / CAMEL SINGLE-DOMAIN ANTI-LYSOZYME / COMPLEX (ANTIBODY-ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) complex | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Camelus dromedarius (Arabian camel) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Desmyter, A. / Transue, T.R. / Arbabi Gharoudi, M. / Dao Thi, M. / Poortmans, F. / Hamers, R. / Muyldermans, S. / Wyns, L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hamers, R. / Muyldermans, S. / Wyns, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mel.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mel.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1mel ftp://data.pdbj.org/pub/pdb/validation_reports/me/1mel | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE ASYMMETRIC UNIT CONTAINS TWO INDEPENDENTLY REFINED COMPLEXES: ANTIBODY A WITH LYSOZYME L AND ANTIBODY B WITH LYSOZYME M. SUBTLE DIFFERENCES BETWEEN THE TWO COMPLEXES HAVE BEEN OBSERVED, BUT HAVE NOT YET BEEN CAREFULLY ANALYZED. |
-Components
#1: Antibody | Mass: 15657.090 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Gene: ANTIBODY VH FRAGMENT CAB-LYS3 / Plasmid: PHEN4 / Production host: Escherichia coli (E. coli) #2: Protein | Mass: 14331.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Tissue: EGG / Description: PURCHASED FROM BOEHRINGER MANNHEIM / Gene: ANTIBODY VH FRAGMENT CAB-LYS3 / Plasmid: PHEN4 / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.4 Details: HANGING DROP, pH 6.4, vapor diffusion - hanging drop | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 2, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 17829 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 84.8 |
Reflection shell | *PLUS % possible obs: 84.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1LYS AND 1IGM Resolution: 2.5→10 Å / σ(F): 0 Details: RESIDUES ASP B 73 - LYS B 76 WERE LEFT IN THE MODEL TO CONSTRAIN RESIDUES 72 AND 77.
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Displacement parameters | Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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