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Yorodumi- PDB-1nmc: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nmc | |||||||||
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Title | COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 15 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE | |||||||||
Components |
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Keywords | COMPLEX (SINGLE-CHAIN ANTIBODY/ANTIGEN) / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) / HYDROLASE / COMPLEX (SINGLE-CHAIN ANTIBODY-ANTIGEN) complex | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza A virus Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Malby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Three-dimensional structures of single-chain Fv-neuraminidase complexes. Authors: Malby, R.L. / McCoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. #1: Journal: Proteins / Year: 1993 Title: Recombinant Antineuraminidase Single Chain Antibody: Expression, Characterization, and Crystallization in Complex with Antigen Authors: Malby, R.L. / Caldwell, J.B. / Gruen, L.C. / Harley, V.R. / Ivancic, N. / Kortt, A.A. / Lilley, G.G. / Power, B.E. / Webster, R.G. / Colman, P.M. / Hudson, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nmc.cif.gz | 256.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmc.ent.gz | 210.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1nmc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1nmc_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 1nmc_validation.cif.gz | 66.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmc ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmc | HTTPS FTP |
-Related structure data
Related structure data | 1a14C 1ncaS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: (Code: given Matrix: (0.998491, 0.05492, -0.000553), Vector: |
-Components
-Protein , 1 types, 2 molecules NA
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 2 / Fragment: RESIDUES 82 - 468 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Genus: Influenzavirus A / Strain: N9 / Variant: A/TERN/AUSTRALIA/G70C/75 / Cell (production host): EGG / Production host: Gallus gallus (chicken) / References: UniProt: P03472, exo-alpha-sialidase |
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-Antibody , 2 types, 4 molecules HBLC
#2: Antibody | Mass: 13399.659 Da / Num. of mol.: 2 Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094 #3: Antibody | Mass: 12162.203 Da / Num. of mol.: 2 Fragment: VH AND VL DOMAINS OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIFTEEN RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094 |
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-Sugars , 3 types, 8 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 182 molecules
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE ...THE THREE OLIGOSACCH |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4 Å3/Da / Density % sol: 70 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION ...Details: NC10 SCFV(15) AND N9 NA WERE MIXED TOGETHER (SCFV(15) IN SLIGHT MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOUR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8. PH range: 6.6-6.8 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Malby, R.L., (1993) Proteins: Struct.,Funct., Genet., 16, 57. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: PHOTON FACTORY / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 67425 / % possible obs: 80 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.104 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 70 |
Reflection | *PLUS Num. measured all: 156708 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NCA Resolution: 2.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 2
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Displacement parameters | Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.65 Å / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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