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Yorodumi- PDB-8wt1: Crystal structure of S9 carboxypeptidase from Geobacillus steroth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wt1 | ||||||
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Title | Crystal structure of S9 carboxypeptidase from Geobacillus sterothermophilus | ||||||
Components | S9 family peptidase | ||||||
Keywords | HYDROLASE / Carboxypeptidase / Prolyl oligopeptidase / Oligomerization / Acylaminoacyl. | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus ATCC 12980 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Chandravanshi, K. / Kumar, A. / Sen, C. / Singh, R. / Bhange, G.B. / Makde, R.D. | ||||||
Funding support | India, 1items
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Citation | Journal: Febs Lett. / Year: 2024 Title: Crystal structure and solution scattering of Geobacillus stearothermophilus S9 peptidase reveal structural adaptations for carboxypeptidase activity. Authors: Chandravanshi, K. / Singh, R. / Bhange, G.N. / Kumar, A. / Yadav, P. / Kumar, A. / Makde, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wt1.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8wt1.ent.gz | 850.6 KB | Display | PDB format |
PDBx/mmJSON format | 8wt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/8wt1 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/8wt1 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 77207.297 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Details: UPI0006AC02FD, WP_053532245 Source: (gene. exp.) Geobacillus stearothermophilus ATCC 12980 (bacteria) Gene: D9548_14720 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3L7D5Q2 |
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-Non-polymers , 6 types, 2194 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-ALA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.4 % |
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Crystal grow | Temperature: 294.15 K / Method: microbatch / pH: 4 Details: 0.8 M Ammonium sulphate, 0.1 M sodium citrate pH-4.0, 20 mM MES, 100 mM NaCl (Mixed in 1:1) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 2, 2022 |
Radiation | Monochromator: Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→48.94 Å / Num. obs: 394267 / % possible obs: 92.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.064 / Rrim(I) all: 0.125 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1 / Num. unique obs: 20613 / CC1/2: 0.527 / Rpim(I) all: 0.74 / Rrim(I) all: 1.424 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.94 Å / SU ML: 0.2946 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1511 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.56 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→48.94 Å
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Refine LS restraints |
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LS refinement shell |
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