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Yorodumi- PDB-1t3f: THREE DIMENSIONAL STRUCTURE OF A HUMANIZED ANTI-IFN-GAMMA FAB (Hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t3f | |||||||||
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Title | THREE DIMENSIONAL STRUCTURE OF A HUMANIZED ANTI-IFN-GAMMA FAB (HuZAF) IN P21 21 21 SPACE GROUP | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Antibody Engineering / Humanized and Chimeric antibody / FAB / Gamma-Interferon | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Bourne, P.C. / Terzyan, S.S. / Cloud, G. / Landolfi, N.F. / Vasquez, M. / Edmundson, A.B. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Three-dimensional structures of a humanized anti-IFN-gamma Fab (HuZAF) in two crystal forms. Authors: Bourne, P.C. / Terzyan, S.S. / Cloud, G. / Landolfi, N.F. / Vasquez, M. / Edmundson, A.B. | |||||||||
History |
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Remark 999 | SEQUENCE THERE IS NO SEQUENCE DATABASE REFERENCE FOR THIS ENTRY. THE SEQUENCE WAS DETERMINED IN THE ...SEQUENCE THERE IS NO SEQUENCE DATABASE REFERENCE FOR THIS ENTRY. THE SEQUENCE WAS DETERMINED IN THE PROTEIN DESIGN LABORATORY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t3f.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t3f.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 1t3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t3f_validation.pdf.gz | 422.9 KB | Display | wwPDB validaton report |
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Full document | 1t3f_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 1t3f_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1t3f_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/1t3f ftp://data.pdbj.org/pub/pdb/validation_reports/t3/1t3f | HTTPS FTP |
-Related structure data
Related structure data | 1t04C 1b4jS C: citing same article (ref.) 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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-Components
#1: Antibody | Mass: 23430.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The source is engineered human constant and framework regions with CDRs from mouse Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q6GMW1 |
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#2: Antibody | Mass: 23480.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The source is engineered human constant and framework regions with CDRs from mouse Source: (gene. exp.) Homo sapiens (human) |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 53.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG6000, SODIUM CITRATE, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC BLUE OPTICS |
Radiation | Monochromator: OSMIC BLUE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 30615 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 25.13 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.15 / Num. unique all: 1518 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B4J Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.796 / SU ML: 0.107 / Isotropic thermal model: Overall anisotropic B-factor / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.071 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.001→2.053 Å / Total num. of bins used: 20 /
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