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Yorodumi- PDB-4re5: Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 4re5 | ||||||
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Title | Acylaminoacyl peptidase complexed with a chloromethylketone inhibitor | ||||||
Components | Acylamino-acid-releasing enzyme | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta-propeller / alpha-beta-hydrolase fold / chloromethyl-ketone inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information acylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å | ||||||
Authors | Menyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: Catalytically distinct states captured in a crystal lattice: the substrate-bound and scavenger states of acylaminoacyl peptidase and their implications for functionality. Authors: Menyhard, D.K. / Orgovan, Z. / Szeltner, Z. / Szamosi, I. / Harmat, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4re5.cif.gz | 451.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4re5.ent.gz | 370 KB | Display | PDB format |
PDBx/mmJSON format | 4re5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4re5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4re5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4re5_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 4re5_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/4re5 ftp://data.pdbj.org/pub/pdb/validation_reports/re/4re5 | HTTPS FTP |
-Related structure data
Related structure data | 4re6C 2hu5S C: citing same article (ref.) 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 8 - 581 / Label seq-ID: 8 - 581
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Details | The biological assembly is dimer consisting of chains A and B of the asymmetric unit. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 63108.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1 Gene: APE_1547.1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YBQ2, acylaminoacyl-peptidase |
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-Non-polymers , 5 types, 669 molecules
#2: Chemical | Type: Peptide-like / Class: Enzyme inhibitor / Mass: 447.912 Da / Num. of mol.: 2 / 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) #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 78 mM sodium acetate buffer, 2.4% w/v PEG Mw4000, 6.7mM dithiothreitol and 0.44 mM EDTA. The protein was co-crystallized with the inhibitor., pH 4.5, 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: mirrors (Blue) |
Radiation | Monochromator: Rigaku confocal Blue optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 90022 / Num. obs: 90022 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.93 % / Biso Wilson estimate: 32.79 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.58 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.81 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6591 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2HU5 Resolution: 1.9→19.93 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.984 / SU ML: 0.117 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 35.253 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.93 Å
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Refine LS restraints |
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