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Yorodumi- PDB-5t1q: 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Ami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5t1q | ||||||
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Title | 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus. | ||||||
Components | N-acetylmuramoyl-L-alanine amidase domain-containing protein SAOUHSC_02979 | ||||||
Keywords | HYDROLASE / N-acetylmuramoyl-L-alanine Amidase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Minasov, G. / Nocadello, S. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bagnoli, F. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 2.15 Angstrom Crystal Structure of N-acetylmuramoyl-L-alanine Amidase from Staphylococcus aureus. Authors: Minasov, G. / Nocadello, S. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bagnoli, F. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t1q.cif.gz | 589.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t1q.ent.gz | 485.9 KB | Display | PDB format |
PDBx/mmJSON format | 5t1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5t1q_validation.pdf.gz | 455.6 KB | Display | wwPDB validaton report |
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Full document | 5t1q_full_validation.pdf.gz | 462.4 KB | Display | |
Data in XML | 5t1q_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 5t1q_validation.cif.gz | 82.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/5t1q ftp://data.pdbj.org/pub/pdb/validation_reports/t1/5t1q | HTTPS FTP |
-Related structure data
Related structure data | 2lrjS 3fi7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 40541.777 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Strain: NCTC 8325 / Gene: SAOUHSC_02979 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q2G222 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-PGE / | #4: 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: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 Details: Protein: 12.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3); Screen: PACT (B2), 0.1M MIB (pH 5.0), 25% (w/v) PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2016 / Details: C(111) |
Radiation | Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 82976 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 11.7 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.132 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 3.8 / CC1/2: 0.877 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FI7, 2LRJ Resolution: 2.15→29.53 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.97 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.189 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.809 Å2
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Refinement step | Cycle: 1 / Resolution: 2.15→29.53 Å
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Refine LS restraints |
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