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Yorodumi- PDB-4gmg: NADP+ bound structure of a Thiazolinyl Imine Reductase from Yersi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gmg | ||||||
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Title | NADP+ bound structure of a Thiazolinyl Imine Reductase from Yersinia enterocolitica (Irp3) | ||||||
Components | Yersiniabactin biosynthetic protein YbtU | ||||||
Keywords | OXIDOREDUCTASE / NADPH-dependent thiazoline reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia enterocolitica subsp. enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Lamb, A.L. / Meneely, K.M. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Two Structures of a Thiazolinyl Imine Reductase from Yersinia enterocolitica Provide Insight into Catalysis and Binding to the Nonribosomal Peptide Synthetase Module of HMWP1. Authors: Meneely, K.M. / Lamb, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gmg.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmg.ent.gz | 227.6 KB | Display | PDB format |
PDBx/mmJSON format | 4gmg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmg ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmg | HTTPS FTP |
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-Related 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: 42926.852 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria) Strain: 33114 / Gene: Irp3, ybtU, YE2619 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A1JTG0 #2: Chemical | ChemComp-NAP / #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: 2.07 Å3/Da / Density % sol: 40.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl pH 8.0, 13% PEG 3350 (w/v), 0.11 M magnesium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97944 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 28, 2012 / Details: mirrors |
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97944 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→39.89 Å / Num. all: 63702 / Num. obs: 63447 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.389 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.31→2.43 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.087 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→39.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.676 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→39.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.306→2.366 Å / Total num. of bins used: 20
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