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Yorodumi- PDB-7l6j: Crystal Structure of the Putative Hydrolase from Stenotrophomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l6j | ||||||
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Title | Crystal Structure of the Putative Hydrolase from Stenotrophomonas maltophilia | ||||||
Components | Putative hydrolase | ||||||
Keywords | HYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative hydrolase | ||||||
Function / homology | isochorismatase activity / Isochorismatase / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / FORMIC ACID / Putative hydrolase Function and homology information | ||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: Crystal Structure of the Putative Hydrolase from Stenotrophomonas maltophilia Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.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 | 7l6j.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l6j.ent.gz | 90.1 KB | Display | PDB format |
PDBx/mmJSON format | 7l6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/7l6j ftp://data.pdbj.org/pub/pdb/validation_reports/l6/7l6j | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24040.498 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria) Strain: K279a / Gene: Smlt2820 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic / References: UniProt: B2FHQ4 | ||||||
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#2: Chemical | ChemComp-CL / | ||||||
#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop Details: Protein: 7.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: ComPAS (H12), 3.0M Sodium formate; Cryo: 4.0M Sodium formate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2020 / Details: Be |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→30 Å / Num. obs: 41390 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.036 / Rrim(I) all: 0.117 / Rsym value: 0.111 / Χ2: 1.276 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2047 / CC1/2: 0.851 / CC star: 0.959 / Rpim(I) all: 0.287 / Rrim(I) all: 0.931 / Rsym value: 0.886 / Χ2: 1.002 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.78→29.45 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.633 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 66.54 Å2 / Biso mean: 19.994 Å2 / Biso min: 12.37 Å2
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Refinement step | Cycle: final / Resolution: 1.78→29.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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