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Yorodumi- PDB-4h4f: Crystal structure of human chymotrypsin C (CTRC) bound to inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4h4f | ||||||
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Title | Crystal structure of human chymotrypsin C (CTRC) bound to inhibitor eglin c from Hirudo medicinalis | ||||||
Components |
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Keywords | hydrolase/hydrolase inhibitor / Serine protease / protease inhibitor / hydrolase-hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information chymotrypsin C / Cobalamin (Cbl, vitamin B12) transport and metabolism / cobalamin metabolic process / serine-type endopeptidase inhibitor activity / response to wounding / intracellular calcium ion homeostasis / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hirudo medicinalis (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å | ||||||
Authors | Batra, J. / Soares, A.S. / Radisky, E.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Long-range Electrostatic Complementarity Governs Substrate Recognition by Human Chymotrypsin C, a Key Regulator of Digestive Enzyme Activation. Authors: Batra, J. / Szabo, A. / Caulfield, T.R. / Soares, A.S. / Sahin-Toth, M. / Radisky, E.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4h4f.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4h4f.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 4h4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4h4f_validation.pdf.gz | 443 KB | Display | wwPDB validaton report |
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Full document | 4h4f_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 4h4f_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 4h4f_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/4h4f ftp://data.pdbj.org/pub/pdb/validation_reports/h4/4h4f | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28054.791 Da / Num. of mol.: 1 / Fragment: Chymotrypsin C (unp residues 30-268) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLCR, CTRC / Strain (production host): HEK 293T / References: UniProt: Q99895, chymotrypsin C | ||||
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#2: Protein | Mass: 8072.089 Da / Num. of mol.: 1 / Fragment: Eglin c (unp residues 8-70) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01051 | ||||
#3: Protein/peptide | Mass: 1030.197 Da / Num. of mol.: 1 / Fragment: CTRC propeptide (unp residues 17-26) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CLCR, CTRC / Strain (production host): HEK 293T / References: UniProt: Q99895, chymotrypsin C | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | CHAIN Q IS A PRO-DOMAIN THAT HAS BEEN CLEAVED UPON ACTIVATION BUT IT IS NOT RELEASED BECAUSE IT ...CHAIN Q IS A PRO-DOMAIN THAT HAS BEEN CLEAVED UPON ACTIVATION | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M lithium sulfate monohydrate, 0.1 M TRIS hydrochloride and 30 % (w/v) PEG 4000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→55.784 Å / Num. all: 27661 / Num. obs: 27661 / % possible obs: 97.34 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 51.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 9 / Rsym value: 0.146 / % possible all: 76.8 |
-Processing
Software |
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Refinement | Resolution: 1.9→55.78 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.753 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.52 Å2 / Biso mean: 25.5891 Å2 / Biso min: 12.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→55.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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