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Yorodumi- PDB-8dor: Crystal structure of Dihydropteridine reductase/oxygen-insensitiv... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dor | |||||||||
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Title | Crystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase from Klebsiella pneumoniae | |||||||||
Components | Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase | |||||||||
Keywords | OXIDOREDUCTASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Oxygen-insensitive NAD(P)H nitroreductase NfsB-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase Function and homology information | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of Dihydropteridine reductase/oxygen-insensitive NAD(P)H nitroreductase from Klebsiella pneumoniae Authors: Lovell, S. / Liu, L. / Seibold, S. / Battaile, K.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dor.cif.gz | 374.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dor.ent.gz | 301.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dor_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8dor_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8dor_validation.xml.gz | 43.1 KB | Display | |
Data in CIF | 8dor_validation.cif.gz | 64.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/8dor ftp://data.pdbj.org/pub/pdb/validation_reports/do/8dor | HTTPS FTP |
-Related structure data
Related structure data | 1icrS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24959.158 Da / Num. of mol.: 4 / Fragment: KlpnC.20499.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: nfnB, KPN_00553, KPHS_29700 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A6T5Y2 #2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.4 Å3/Da / Density % sol: 48.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: JCSG+ D12: 16% (w/v) PEG 8000; 20% (v/v) glycerol, 0.04 M K2HPO4, KlpnC.20499.a.B1.PW39082 at 30 mg/mL, Tray: plate 12477 well D12 drop 2, Puck: PSL1107, Cryo: DIRECT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 24, 2022 | |||||||||||||||||||||||||||
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.35→49.21 Å / Num. obs: 204417 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.032 / Rrim(I) all: 0.106 / Net I/σ(I): 13.5 / Num. measured all: 2214463 / Scaling rejects: 56 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.9
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ICR Resolution: 1.35→29.47 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.34 Å2 / Biso mean: 16.6858 Å2 / Biso min: 6.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.35→29.47 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
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