+Open data
-Basic information
Entry | Database: PDB / ID: 5tl5 | |||||||||
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Title | COMPLEX BETWEEN HUMAN CD27 AND ANTIBODY M2177 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity ...TNFs bind their physiological receptors / negative regulation of T cell apoptotic process / positive regulation of T cell differentiation / positive regulation of B cell differentiation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / immunoglobulin mediated immune response / extrinsic apoptotic signaling pathway / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / transmembrane signaling receptor activity / response to ethanol / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of apoptotic process / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. | |||||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017 Title: Crystal structure of CD27 in complex with a neutralizing noncompeting antibody. Authors: Teplyakov, A. / Obmolova, G. / Malia, T.J. / Gilliland, G.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tl5.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tl5.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/5tl5 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/5tl5 | HTTPS FTP |
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-Related structure data
Related structure data | 1iqwS 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
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23712.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 24444.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus, Homo sapiens / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) |
-Protein / Sugars , 2 types, 2 molecules A
#3: Protein | Mass: 12287.896 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 21-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CD27, TNFRSF7 / Production host: unidentified baculovirus / References: UniProt: P26842 |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 306 molecules
#4: Chemical | ChemComp-SO4 / |
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#6: 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: 2.58 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES PH 6.5, 17% PEG 4000, 0.2 M AMMONIUM CITRATE PH range: 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 56791 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 4.1 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IQW Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.761 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.119
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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