+Open data
-Basic information
Entry | Database: PDB / ID: 8h7p | ||||||
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Title | Crystal structure of aqualigase bound with Suc-AAPF | ||||||
Components |
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Keywords | HYDROLASE / subtilisin / Ser protease / structure based engineering / peptide synthesis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) Synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Li, H. / Ma, M.Z. / Zhang, L.J. / Dai, L. / Chen, C.-C. / Guo, R.-T. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystal structure of aqualigase bound with Suc-AAPF Authors: Li, H. / Ma, M.Z. / Zhang, L.J. / Dai, L. / Chen, C.-C. / Guo, R.-T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h7p.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h7p.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 8h7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h7p_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 8h7p_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 8h7p_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 8h7p_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/8h7p ftp://data.pdbj.org/pub/pdb/validation_reports/h7/8h7p | HTTPS FTP |
-Related structure data
Related structure data | 1to1S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28363.553 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: KS08_04965 / Production host: Bacillus subtilis (bacteria) / References: UniProt: A0A7U5AV24, subtilisin |
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#2: Protein/peptide | Mass: 502.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others) |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-PGE / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.96 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / Details: 25% isopropanol, 28% PEG 3350, 0.1 M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Sep 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.34138 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→37.06 Å / Num. obs: 17217 / % possible obs: 97.3 % / Redundancy: 4.8 % / CC1/2: 0.997 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.82→1.85 Å / Num. unique obs: 806 / CC1/2: 0.978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TO1 Resolution: 1.82→37.06 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.1969 / WRfactor Rwork: 0.1412 / FOM work R set: 0.8876 / SU B: 2.957 / SU ML: 0.09 / SU R Cruickshank DPI: 0.1609 / SU Rfree: 0.1405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.14 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.11 Å2 / Biso mean: 10.87 Å2 / Biso min: 5.58 Å2
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Refinement step | Cycle: final / Resolution: 1.82→37.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.867 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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