+Open data
-Basic information
Entry | Database: PDB / ID: 1h4w | ||||||
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Title | Structure of human trypsin IV (brain trypsin) | ||||||
Components | TRYPSIN IVA | ||||||
Keywords | HYDROLASE / SERINE PROTEASE / SIGNAL TRANSDUCTION / INHIBITOR RESISTANCE / ALZHEIMER DISEASE | ||||||
Function / homology | Function and homology information Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / endothelial cell migration / trypsin / digestion / serine-type peptidase activity / tertiary granule lumen ...Uptake of dietary cobalamins into enterocytes / antimicrobial humoral response / Alpha-defensins / zymogen activation / Antimicrobial peptides / endothelial cell migration / trypsin / digestion / serine-type peptidase activity / tertiary granule lumen / serine-type endopeptidase activity / calcium ion binding / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Katona, G. / Berglund, G.I. / Hajdu, J. / Graf, L. / Szilagyi, L. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2002 Title: Crystal structure reveals basis for the inhibitor resistance of human brain trypsin. Authors: Katona, G. / Berglund, G.I. / Hajdu, J. / Graf, L. / Szilagyi, L. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h4w.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h4w.ent.gz | 43.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h4/1h4w ftp://data.pdbj.org/pub/pdb/validation_reports/h4/1h4w | HTTPS FTP |
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-Related structure data
Related structure data | 1trnS 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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Unit cell |
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-Components
#1: Protein | Mass: 24301.510 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: BENZAMIDINE / Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Variant: A FORM / Plasmid: PET17B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35030, trypsin |
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#2: Chemical | ChemComp-BEN / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | VAL A 86, CLONING ARTIFACT OR NATURAL POLYMORPHI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: HANGING DROP VAPOUR DIFFUSION 3.3 MG/ML PROTEIN, 2% PEG 4000, 0.05M TRIS PH7.7, 2.5MM CACL2, 2.5 MG/ML BENZAMIDINE/HCL, 25 C, pH 7.70 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.886 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 4, 2000 / Details: MIRRORS |
Radiation | Monochromator: SI 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.886 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→52.7 Å / Num. obs: 26174 / % possible obs: 94.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.5 / % possible all: 92 |
Reflection | *PLUS Num. measured all: 111768 |
Reflection shell | *PLUS % possible obs: 92 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TRN Resolution: 1.7→52.7 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.8756 Å2 / ksol: 0.359685 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→52.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 26170 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.23 |