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Yorodumi- PDB-4gmf: Apo Structure of a Thiazolinyl Imine Reductase from Yersinia ente... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gmf | ||||||
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Title | Apo Structure of a Thiazolinyl Imine Reductase from Yersinia enterocolitica (Irp3) | ||||||
Components | Yersiniabactin biosynthetic protein YbtU | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / NADPH dependent thiazoline reductase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia enterocolitica subsp. enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 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 | 4gmf.cif.gz | 274.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gmf.ent.gz | 222.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gm/4gmf ftp://data.pdbj.org/pub/pdb/validation_reports/gm/4gmf | 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: 41713.480 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: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A1JTG0 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EPE / | #5: 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: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 0.1 M HEPES pH 7.3, 32% PEG 3350 (w/v), 0.25 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 303K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.000034,0.97915,0.97944,0.91837 | |||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 29, 2008 | |||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.85→76.03 Å / Num. obs: 122197 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.395 / Net I/σ(I): 12.4 | |||||||||||||||
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.054 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: SeMet Irp3 Resolution: 1.85→40.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.156 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.14 / 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: 28.287 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→40.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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