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Yorodumi- PDB-6o21: Crystal Structure of Human KLK4 in Complex With Cleaved SFTI-FCQR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o21 | ||||||
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Title | Crystal Structure of Human KLK4 in Complex With Cleaved SFTI-FCQR(Asn14)[1,14] Inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE Inhibitor / Kallikrein-related peptidase 4 / KLK4 / Sunflower Trypsin Inhibitor / SFTI / Laskowski mechanism inhibitor / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information biomineral tissue development / amelogenesis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extracellular matrix disassembly / serine-type peptidase activity / secretory granule / protein catabolic process / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Helianthus annuus (common sunflower) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å | ||||||
Authors | Ilyichova, O.V. / 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 | 6o21.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o21.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 6o21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o21_validation.pdf.gz | 455.9 KB | Display | wwPDB validaton report |
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Full document | 6o21_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 6o21_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | 6o21_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o2/6o21 ftp://data.pdbj.org/pub/pdb/validation_reports/o2/6o21 | HTTPS FTP |
-Related structure data
Related structure data | 4kelSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23926.010 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLK4, KLNB1, hCG_1641510 / Plasmid: pET12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C4DFQ5, UniProt: Q9Y5K2*PLUS | ||||||
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#2: Protein/peptide | | ||||||
#3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 30 % (w/v) PEG 8000, 0.1 M sodium acetate, 0.2 M lithium sulfate, pH 4.5 PH range: 4.5-4.8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→63.15 Å / Num. obs: 62317 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.031 / Rrim(I) all: 0.068 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.368 / Num. unique obs: 3008 / CC1/2: 0.883 / Rpim(I) all: 0.227 / Rrim(I) all: 0.434 / % possible all: 93.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KEL Resolution: 1.15→37.085 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 14.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.23 Å2 / Biso mean: 12.8976 Å2 / Biso min: 3.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→37.085 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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