+Open data
-Basic information
Entry | Database: PDB / ID: 4gwn | |||||||||
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Title | Crystal structure of human mature meprin beta | |||||||||
Components | Meprin A subunit beta | |||||||||
Keywords | HYDROLASE / Multidomain structure | |||||||||
Function / homology | Function and homology information meprin B / meprin A complex / metalloendopeptidase activity / inflammatory response / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Arolas, J.L. / Broder, C. / Jefferson, T. / Guevara, T. / Sterchi, E.E. / Bode, W. / Stocker, W. / Becker-Pauly, C. / Gomis-Ruth, F.X. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis for the sheddase function of human meprin beta metalloproteinase at the plasma membrane Authors: Arolas, J.L. / Broder, C. / Jefferson, T. / Guevara, T. / Sterchi, E.E. / Bode, W. / Stocker, W. / Becker-Pauly, C. / Gomis-Ruth, F.X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gwn.cif.gz | 251.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gwn.ent.gz | 205.3 KB | Display | PDB format |
PDBx/mmJSON format | 4gwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4gwn_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 4gwn_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 4gwn_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 4gwn_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/4gwn ftp://data.pdbj.org/pub/pdb/validation_reports/gw/4gwn | HTTPS FTP |
-Related structure data
Related structure data | 4gwmSC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 62805.758 Da / Num. of mol.: 1 Fragment: Mature meprin beta ectomoiety, UNP residues 62-614 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEP1B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16820, meprin B |
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-Sugars , 5 types, 7 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #8: Sugar | |
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-Non-polymers , 3 types, 3 molecules
#6: Chemical | ChemComp-CD / |
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#7: Chemical | ChemComp-NA / |
#9: Chemical | ChemComp-GOL / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 20%(wt/vol) PEG 3350, 0.2M sodium malonate, 0.1M bis-Tris propane, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.2818 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2011 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2818 Å / Relative weight: 1 |
Reflection | Resolution: 3→48.2 Å / Num. all: 18106 / Num. obs: 18106 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 93.59 Å2 / Rmerge(I) obs: 0.106 |
Reflection shell | Resolution: 3→3.16 Å / Rmerge(I) obs: 0.106 / Num. unique all: 18106 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GWM Resolution: 3→48.16 Å / Cor.coef. Fo:Fc: 0.9023 / Cor.coef. Fo:Fc free: 0.8836 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 197.58 Å2 / Biso mean: 113.27 Å2 / Biso min: 76.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.832 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.18 Å / Total num. of bins used: 9
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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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