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Yorodumi- PDB-4kel: Atomic resolution crystal structure of Kallikrein-Related Peptida... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kel | ||||||
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Title | Atomic resolution crystal structure of Kallikrein-Related Peptidase 4 complexed with a modified SFTI inhibitor FCQR(N) | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Bowman-Birk Inhibitor / Protease / Protease Inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding ...biomineral tissue development / amelogenesis / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / serine-type endopeptidase inhibitor activity / protease binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Helianthus annuus (common sunflower) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.148 Å | ||||||
Authors | Ilyichova, O.V. / Swedberg, J.E. / de Veer, S.J. / Sit, K.C. / Harris, J.M. / Buckle, A.M. | ||||||
Citation | Journal: Biochemistry / Year: 2019 Title: KLK4 Inhibition by Cyclic and Acyclic Peptides: Structural and Dynamical Insights into Standard-Mechanism Protease Inhibitors. Authors: Riley, B.T. / Ilyichova, O. / de Veer, S.J. / Swedberg, J.E. / Wilson, E. / Hoke, D.E. / Harris, J.M. / Buckle, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kel.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kel.ent.gz | 84.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kel.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kel_validation.pdf.gz | 416.2 KB | Display | wwPDB validaton report |
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Full document | 4kel_full_validation.pdf.gz | 417 KB | Display | |
Data in XML | 4kel_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 4kel_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ke/4kel ftp://data.pdbj.org/pub/pdb/validation_reports/ke/4kel | HTTPS FTP |
-Related structure data
Related structure data | 6o21C 2bdgS 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
#1: Protein | Mass: 23926.010 Da / Num. of mol.: 1 / Fragment: Related Peptidase 4, UNP residues 31-253 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4 / Plasmid: pET12a-proPSA-hK4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9Y5K2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Type: Cyclic peptide / Class: Trypsin inhibitor / Mass: 1579.863 Da / Num. of mol.: 1 / Mutation: modified FCQR(N) / Source method: obtained synthetically / Details: modified Sunflower Trypsin Inhibitor / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1 |
#3: Water | ChemComp-HOH / |
Sequence details | THIS SEQUENCE IS NATURAL VARIANT (VARIANT RS2569527) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M lithium sulfate, 0.1M sodium acetate, 30% PEG 8000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2011 | |||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95369 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.148→63.37 Å / Num. all: 64890 / Num. obs: 64890 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 5.978 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 10.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BDG Resolution: 1.148→37.154 Å / Occupancy max: 1 / Occupancy min: 0.11 / FOM work R set: 0.9255 / SU ML: 0.09 / σ(F): 1.36 / Phase error: 14.31 / Stereochemistry target values: MLHL
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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 max: 39.72 Å2 / Biso mean: 12.4673 Å2 / Biso min: 4.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.148→37.154 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24
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