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Yorodumi- PDB-4u2w: Atomic resolution crystal structure of HV-BBI protease inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4u2w | |||||||||
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Title | Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin | |||||||||
Components |
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Keywords | Hydrolase/inhibitor / inhibitor / Hydrolase-inhibitor complex | |||||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / defense response to Gram-negative bacterium / endopeptidase activity / defense response to Gram-positive bacterium / serine-type endopeptidase activity / proteolysis / extracellular space ...trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / defense response to Gram-negative bacterium / endopeptidase activity / defense response to Gram-positive bacterium / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) Odorrana versabilis (bamboo leaf odorous frog) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | |||||||||
Authors | Grudnik, P. / Golik, P. / Malicki, S. / Debowski, D. / Legowska, A. / Rolka, K. / Dubin, G. | |||||||||
Funding support | Poland, 2items
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Citation | Journal: Proteins / Year: 2015 Title: Atomic resolution crystal structure of HV-BBI protease inhibitor from amphibian skin in complex with bovine trypsin. Authors: Grudnik, P. / Debowski, D. / Legowska, A. / Malicki, S. / Golik, P. / Karna, N. / Rolka, K. / Dubin, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u2w.cif.gz | 126.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u2w.ent.gz | 96 KB | Display | PDB format |
PDBx/mmJSON format | 4u2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u2w_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 4u2w_full_validation.pdf.gz | 460 KB | Display | |
Data in XML | 4u2w_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4u2w_validation.cif.gz | 24.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/4u2w ftp://data.pdbj.org/pub/pdb/validation_reports/u2/4u2w | HTTPS FTP |
-Related structure data
Related structure data | 1sfiS 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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2 |
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Unit cell |
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-Components
-Protein/peptide / Protein , 2 types, 2 molecules BA
#1: Protein/peptide | Mass: 1835.262 Da / Num. of mol.: 1 / Fragment: UNP residues 46-61 / Source method: obtained synthetically Source: (synth.) Odorrana versabilis (bamboo leaf odorous frog) References: UniProt: B1VC43 |
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#2: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
-Non-polymers , 4 types, 360 molecules
#3: Chemical | ChemComp-CA / | ||
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#4: Chemical | ChemComp-SO4 / | ||
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
-Details
Has protein modification | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 4.6 Details: sodium acetate trihydrate (0,1 M) at pH 4.6, amonium sulfate (0.3 M) and polyethylene glycol 8000 (30%) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1→46.51 Å / Num. obs: 142495 / % possible obs: 98.09 % / Redundancy: 13 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 30.57 |
Reflection shell | Resolution: 1→1.036 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 6.05 / % possible all: 94.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SFI Resolution: 1→46.51 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.289 / SU ML: 0.007 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.955 Å2
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Refinement step | Cycle: 1 / Resolution: 1→46.51 Å
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Refine LS restraints |
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