+Open data
-Basic information
Entry | Database: PDB / ID: 5hdp | ||||||
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Title | Hydrolase StnA mutant - S185A | ||||||
Components | Hydrolase | ||||||
Keywords | HYDROLASE / Complex | ||||||
Function / homology | Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Chem-STM / Hydrolase Function and homology information | ||||||
Biological species | Streptomyces flocculus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Qian, T. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode Authors: Qian, T. / Wo, J. / Zhang, Y. / Song, Q. / Feng, G. / Luo, R. / Lin, S. / Wu, G. / Chen, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hdp.cif.gz | 422.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hdp.ent.gz | 347.5 KB | Display | PDB format |
PDBx/mmJSON format | 5hdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/5hdp ftp://data.pdbj.org/pub/pdb/validation_reports/hd/5hdp | HTTPS FTP |
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-Related structure data
Related structure data | 5hdfSC 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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Unit cell |
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-Components
#1: Protein | Mass: 40983.809 Da / Num. of mol.: 7 / Mutation: S185A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces flocculus (bacteria) / Gene: stnA Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: L7PIJ2 #2: Chemical | ChemComp-STM / #3: 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: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop Details: 0.1 M Ammonium Citrate dibasic, 0.1 M Sodium citrate pH 5.0, 20% 2-propanol, 15% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9818 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 31, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9818 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 57747 / % possible obs: 95.8 % / Redundancy: 3.2 % / Net I/σ(I): 6.12 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.54 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HDF Resolution: 2.9→46.072 Å / Cor.coef. Fo:Fc: 0.871 / Cor.coef. Fo:Fc free: 0.823 / SU B: 23.518 / SU ML: 0.45 / Cross valid method: THROUGHOUT / ESU R Free: 0.51 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.566 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→46.072 Å
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Refine LS restraints |
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