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- PDB-6bx8: Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway In... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bx8 | |||||||||
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Title | Human Mesotrypsin (PRSS3) Complexed with Tissue Factor Pathway Inhibitor Variant (TFPI1-KD1-K15R-I17C-I34C) | |||||||||
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![]() | HYDROLASE / Hydrolase Inhibitor | |||||||||
Function / homology | ![]() Uptake of dietary cobalamins into enterocytes / negative regulation of blood coagulation / antimicrobial humoral response / Alpha-defensins / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Antimicrobial peptides / cellular response to steroid hormone stimulus / endopeptidase inhibitor activity / endothelial cell migration ...Uptake of dietary cobalamins into enterocytes / negative regulation of blood coagulation / antimicrobial humoral response / Alpha-defensins / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Antimicrobial peptides / cellular response to steroid hormone stimulus / endopeptidase inhibitor activity / endothelial cell migration / trypsin / side of membrane / digestion / serine-type peptidase activity / caveola / serine-type endopeptidase inhibitor activity / blood coagulation / tertiary granule lumen / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / cell surface / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Coban, M. / Sankaran, B. / Cohen, I. / Hockla, A. / Papo, N. / Radisky, E.S. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Disulfide engineering of human Kunitz-type serine protease inhibitors enhances proteolytic stability and target affinity toward mesotrypsin. Authors: Cohen, I. / Coban, M. / Shahar, A. / Sankaran, B. / Hockla, A. / Lacham, S. / Caulfield, T.R. / Radisky, E.S. / Papo, N. #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008 Title: Model preparation in MOLREP and examples of model improvement using X-ray data. Authors: Lebedev, A.A. / Vagin, A.A. / Murshudov, G.N. #2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 1997 Title: Refinement of macromolecular structures by the maximum-likelihood method. Authors: Murshudov, G.N. / Vagin, A.A. / Dodson, E.J. #3: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2004 Title: Coot: model-building tools for molecular graphics. Authors: Paul Emsley / Kevin Cowtan / ![]() Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality ...CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'. #4: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010 Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution. Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart / ![]() Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms. #5: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2010 Title: MolProbity: all-atom structure validation for macromolecular crystallography. Authors: Chen, V.B. / Arendall, W.B. / Headd, J.J. / Keedy, D.A. / Immormino, R.M. / Kapral, G.J. / Murray, L.W. / Richardson, J.S. / Richardson, D.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 610.2 KB | Display | ![]() |
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PDB format | ![]() | 513.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 497.3 KB | Display | ![]() |
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Full document | ![]() | 503.2 KB | Display | |
Data in XML | ![]() | 48.6 KB | Display | |
Data in CIF | ![]() | 70.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6harC ![]() 3p95S ![]() 4bqdS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24257.457 Da / Num. of mol.: 4 / Mutation: S257A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 9681.825 Da / Num. of mol.: 4 / Mutation: K64R, M66C, I83C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.2M Lithium Sulfate, 0.1M BIS-Tris-HCl pH 4.6, 25% v/v PEG 3350 (Anatrace Top96-27) |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: LN2 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→60.0901 Å / Num. obs: 70450 / % possible obs: 97.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 19.36 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.067 / Rrim(I) all: 0.095 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.249 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7014 / CC1/2: 0.887 / Rpim(I) all: 0.249 / Rrim(I) all: 0.352 / % possible all: 93.7 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.58
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P95, 4BQD Resolution: 1.98→60.062 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 22.69 / 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 max: 92.38 Å2 / Biso mean: 30.0686 Å2 / Biso min: 9.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.98→60.062 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24
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