+Open data
-Basic information
Entry | Database: PDB / ID: 1nqb | ||||||
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Title | TRIVALENT ANTIBODY FRAGMENT | ||||||
Components | SINGLE-CHAIN ANTIBODY FRAGMENT | ||||||
Keywords | IMMUNOGLOBULIN / ANTIBODY FRAGMENT / MULTIVALENT ANTIBODY / DIABODY / DOMAIN SWAPPING | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Williams, R.L. / Pei, X.Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3. Authors: Pei, X.Y. / Holliger, P. / Murzin, A.G. / Williams, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nqb.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nqb.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 1nqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nqb_validation.pdf.gz | 431.7 KB | Display | wwPDB validaton report |
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Full document | 1nqb_full_validation.pdf.gz | 435.4 KB | Display | |
Data in XML | 1nqb_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 1nqb_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/1nqb ftp://data.pdbj.org/pub/pdb/validation_reports/nq/1nqb | HTTPS FTP |
-Related structure data
Related structure data | 1jel S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper: (Code: given Matrix: (0.281213, 0.959633, -0.004829), Vector: |
-Components
#1: Antibody | Mass: 28377.535 Da / Num. of mol.: 2 Fragment: VH DOMAIN RESIDUES 2 - 120, VL DOMAIN RESIDUES 121 - 233 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Cell line: NQ11 MURINE-MURINE HYBRIDOMA, B1-8 MURINE-MURINE HYBRIDOMA Gene: B1-8 VH DOMAIN FUSED TO NQ11 V / Plasmid: B18NQ11 / Cellular location (production host): SECRETED Gene (production host): B1-8 VH DOMAIN FUSED TO NQ11 VL DOMAIN Production host: Escherichia coli (E. coli) / Strain (production host): TG1TR / References: UniProt: P01751 #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 30% 2-PROPANOL, 0.2M NA CITRATE, 0.1M NA CACODYLATE PH 6.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1994 / Details: MIRRORS |
Radiation | Monochromator: BENT CYLINDRICAL GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 33839 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 12 / Rsym value: 0.174 / % possible all: 98.1 |
Reflection | *PLUS Num. measured all: 95579 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JEL 1jel Resolution: 2→6 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: INDIVIDUAL ISOTROPIC B FA / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 12.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 6 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1 / Weight position: 300
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 31030 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.271 |