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Yorodumi- PDB-4hxf: Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hxf | ||||||
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Title | Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone | ||||||
Components | Putative uncharacterized protein PH0594 | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / self-compartmentalization / beta-propeller / alpha/beta hyrdolase fold / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.601 Å | ||||||
Authors | Kiss-Szeman, A. / Menyhard, D.K. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION. Authors: Menyhard, D.K. / Kiss-Szeman, A. / Tichy-Racs, E. / Hornung, B. / Radi, K. / Szeltner, Z. / Domokos, K. / Szamosi, I. / Naray-Szabo, G. / Polgar, L. / Harmat, V. #1: Journal: Biochim.Biophys.Acta / Year: 2009 Title: Characterization of a novel acylaminoacyl peptidase with hexameric structure and endopeptidase activity. Authors: Szeltner, Z. / Kiss, A.L. / Domokos, K. / Harmat, V. / Naray-Szabo, G. / Polgar, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hxf.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hxf.ent.gz | 223.3 KB | Display | PDB format |
PDBx/mmJSON format | 4hxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hx/4hxf ftp://data.pdbj.org/pub/pdb/validation_reports/hx/4hxf | HTTPS FTP |
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-Related structure data
Related structure data | 4hxeSC 4hxgC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules B
#1: Protein | Mass: 73336.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3 Gene: PH0594 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O58323, acylaminoacyl-peptidase |
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-Non-polymers , 5 types, 672 molecules
#2: Chemical | ChemComp-Y3A / Type: Peptide-like / Class: Enzyme inhibitor / Mass: 447.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26ClN3O5 Details: The chlorormethyl ketone inhibitor linked to the protein through two covalent bonds with the active site serine and histidine References: Z-GLY-GLY-PHE-CHLOROMETHYL KETONE (BOUND FORM) | ||||||
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#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-HEZ / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.5 M 1,6-hexanediol, 0.20 M MgCl2, 0.1 M Tris/HCl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 15, 2010 / Details: confocal mirrors |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 122438 / Num. obs: 122438 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.03 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.25 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 5.24 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 2.57 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HXE Resolution: 1.601→19.74 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.824 / SU ML: 0.048 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HEZ B711 AND WATER B1336 LIE ON A TWOFOLD AXIS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.811 Å2
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Refinement step | Cycle: LAST / Resolution: 1.601→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.601→1.643 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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