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Yorodumi- PDB-4d3z: The structure of inactive prolegumain from chinese hamster, trigo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d3z | |||||||||
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Title | The structure of inactive prolegumain from chinese hamster, trigonal space group. | |||||||||
Components | PROLEGUMAIN | |||||||||
Keywords | HYDROLASE / LEGUMAIN / CYSTEINE PROTEASE / SUCCINIMIDE / ASPARAGINYL ENDOPEPTIDASE / CHO | |||||||||
Function / homology | Function and homology information negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / positive regulation of endothelial cell chemotaxis ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / receptor catabolic process / self proteolysis / response to acidic pH / dendritic spine organization / positive regulation of monocyte chemotaxis / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / endopeptidase activator activity / cellular response to calcium ion / lysosomal lumen / positive regulation of mitotic cell cycle / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / negative regulation of neuron apoptotic process / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / extracellular region Similarity search - Function | |||||||||
Biological species | CRICETULUS GRISEUS (Chinese hamster) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Li, W. / Heinz, D.W. / Krausze, J. | |||||||||
Citation | Journal: To be Published Title: A Detailed Look Into Chinese Hamster Legumain Active Site Structure and Exploration of its Function Authors: Li, W. / Damme, M. / Buessow, K. / Grimm, I. / Van Den Heuvel, J. / Heinz, D.W. / Krausze, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d3z.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d3z.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 4d3z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d3z_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 4d3z_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 4d3z_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 4d3z_validation.cif.gz | 21.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/4d3z ftp://data.pdbj.org/pub/pdb/validation_reports/d3/4d3z | HTTPS FTP |
-Related structure data
Related structure data | 4d3xC 4d3yC 4fguS 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: Protein | Mass: 46625.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) CRICETULUS GRISEUS (Chinese hamster) / Cell line: LEC3.8.2.1 / Organ: OVARY / References: UniProt: G3I1H5, legumain | ||
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#2: Sugar | #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: 2.03 Å3/Da / Density % sol: 39.5 % / Description: NONE |
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Crystal grow | pH: 8 Details: 0.03 M MGCL2, 0.03 M CACL2, 10%(W/V) PEG 20000, 20%(V/V) PEG 550 MME, 0.1 MOPS/HEPES PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033191 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033191 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 17828 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 19.3 % / Biso Wilson estimate: 40.26 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 18.1 % / Rmerge(I) obs: 1.269 / Mean I/σ(I) obs: 2.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FGU Resolution: 2.3→19.824 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.824 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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