+Open data
-Basic information
Entry | Database: PDB / ID: 2d03 | ||||||
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Title | Crystal structure of the G91S mutant of the NNA7 Fab | ||||||
Components | (anti-glycophorin A type N immunoglobulin ...) x 2 | ||||||
Keywords | IMMUNE SYSTEM / antibody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / : Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Xie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Crystallographic analysis of the NNA7 Fab and proposal for the mode of human blood-group recognition. Authors: Xie, K. / Song, S.C. / Spitalnik, S.L. / Wedekind, J.E. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Purification, crystallization and X-ray diffraction analysis of a recombinant Fab that recognizes a human blood-group antigen Authors: Song, S.C. / Xie, K. / Czerwinski, M. / Spitalnik, S.L. / Wedekind, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d03.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d03.ent.gz | 79.1 KB | Display | PDB format |
PDBx/mmJSON format | 2d03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/2d03 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/2d03 | HTTPS FTP |
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-Related structure data
Related structure data | 1t2qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | One L-chain and one H-chain compose the Fab fragment |
-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23898.514 Da / Num. of mol.: 1 / Mutation: G91S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOM3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE |
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#2: Antibody | Mass: 23762.494 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pCOM3H / Production host: Escherichia coli (E. coli) / Strain (production host): SURE / References: GenBank: 68144533 |
-Non-polymers , 4 types, 312 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-MES / | #5: Chemical | ChemComp-PEG / | #6: 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: 2.71 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 5000 MME, (NH4)2SO4, MES, YCl3, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 4, 2004 / Details: mirrors |
Radiation | Monochromator: Horizontal focusing, 5.05 asymmetric cut Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→24.44 Å / Num. all: 147694 / Num. obs: 35107 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.21 % / Biso Wilson estimate: 22.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4379 / Rsym value: 0.424 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1T2Q Resolution: 1.97→24.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1788620.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.3098 Å2 / ksol: 0.391093 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→24.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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