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Yorodumi- PDB-3ffd: Structure of parathyroid hormone-related protein complexed to a n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ffd | ||||||
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Title | Structure of parathyroid hormone-related protein complexed to a neutralizing monoclonal antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HORMONE / pthrp complexed to fab / Cleavage on pair of basic residues / Hormone / Nucleus / Secreted / IMMUNE SYSTEM-HORMONE COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / cAMP metabolic process / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / osteoblast development / peptide hormone receptor binding / bone mineralization / epidermis development / skeletal system development / female pregnancy / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / cell-cell signaling / G alpha (s) signalling events / regulation of gene expression / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Golgi apparatus / extracellular space / extracellular region / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Mckinstry, W.J. / Polekhina, G. / Diefenbach-Jagger, H. / Ho, P.W.M. / Sato, K. / Onuma, E. / Gillespie, M.T. / Martin, T.J. / Parker, M.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structural basis for antibody discrimination between two hormones that recognize the parathyroid hormone receptor Authors: McKinstry, W.J. / Polekhina, G. / Diefenbach-Jagger, H. / Ho, P.W.M. / Sato, K. / Onuma, E. / Gillespie, M.T. / Martin, T.J. / Parker, M.W. #1: Journal: J.Biol.Chem. / Year: 2001 Title: Multiple sites of contact between the carboxyl-terminal binding domain of PTHrP-(1--36) analogs and the amino-terminal extracellular domain of the PTH/PTHrP receptor identified by photoaffinity cross-linking Authors: Gensure, R.C. / Gardella, T.J. / Juppner, H. #2: Journal: Trends Endocrinol.Metab. / Year: 2001 Title: Molecular properties of the PTH/PTHrP receptor Authors: Gardella, T.J. / Juppner, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ffd.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ffd.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ffd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/3ffd ftp://data.pdbj.org/pub/pdb/validation_reports/ff/3ffd | HTTPS FTP |
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-Related 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: 23340.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell Cellular location (production host): abdominal cavity of balb/c Production host: mus musculus (house mouse) |
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#2: Antibody | Mass: 23751.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell Cellular location (production host): abdominal cavity of balb/c Production host: mus musculus (house mouse) |
#3: Protein | Mass: 12597.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12272 |
#4: 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: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: PEG 400, TRIS, pH 8.70, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 / Wavelength: 0.99988 Å | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2001 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2→30 Å / Num. all: 42014 / Num. obs: 42012 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 29.03 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 27.8 | |||||||||
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4138 / Rsym value: 0.696 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IGT AND 1IGC Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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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→2.13 Å
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