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Yorodumi- PDB-4s24: 1.7 Angstrom Crystal Structure of of Putative Modulator of Drug A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s24 | ||||||
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Title | 1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92 | ||||||
Components | Modulator of drug activity B | ||||||
Keywords | OXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / FLAVODOXIN-LIKE FOLD / NADPH DEHYDROGENASE (QUINONE) ACTIVITY / FLAVIN ADENINE DINUCLEOTIDE BINDING | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis CO92 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 1.7 Angstrom Crystal Structure of of Putative Modulator of Drug Activity (apo- form) from Yersinia pestis CO92. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / 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 | 4s24.cif.gz | 97.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4s24.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 4s24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/4s24 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/4s24 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22609.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Strain: CO92 / Gene: mdaB / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7CGH8, UniProt: A0A2U2H1J1*PLUS |
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-Non-polymers , 5 types, 180 molecules
#2: Chemical | ChemComp-SO4 / | ||||
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#3: Chemical | ChemComp-PGE / | ||||
#4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: Protein: 10.2 mg/ml, 0.1M Tris HCl (pH 8.3), Screen: JSCG+ (C6), 0.1M Phosphate-citrate (pH 4.2), 40% (v/v) PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-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: Dec 11, 2014 / Details: beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 29069 / Num. obs: 29069 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 62.5 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 15.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 6.2 / Num. unique all: 1417 / Rsym value: 0.56 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→29.41 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.776 / SU ML: 0.045 Isotropic thermal model: Thermal Factors Individually Isotropically Refined Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.075 / 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: 33.702 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / 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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