+Open data
-Basic information
Entry | Database: PDB / ID: 3qmw | ||||||
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Title | RedJ with PEG molecule bound in the active site | ||||||
Components | Thioesterase | ||||||
Keywords | HYDROLASE / Alpha/Beta hydrolase fold | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Whicher, J.R. / Smith, J.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structure and Function of the RedJ Protein, a Thioesterase from the Prodiginine Biosynthetic Pathway in Streptomyces coelicolor. Authors: Whicher, J.R. / Florova, G. / Sydor, P.K. / Singh, R. / Alhamadsheh, M. / Challis, G.L. / Reynolds, K.A. / Smith, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qmw.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qmw.ent.gz | 159.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qm/3qmw ftp://data.pdbj.org/pub/pdb/validation_reports/qm/3qmw | HTTPS FTP |
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-Related structure data
Related structure data | 3qmvSC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28639.441 Da / Num. of mol.: 4 / Fragment: UNP residues 6-261 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCO5894, SC3F7.14 / Production host: Escherichia coli (E. coli) References: UniProt: O54157, Hydrolases; Acting on ester bonds; Thioester hydrolases #2: Chemical | ChemComp-PG4 / | #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: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG3350, 0.22 M sodium chloride, 2 mM DTT, 0.1 M HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 16, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 35740 / Num. obs: 33414 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 0.101 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.359 / % possible all: 83.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QMV Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / ESU R: 3.878 / ESU R Free: 0.37 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.475 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.564 Å / Total num. of bins used: 20
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