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Yorodumi- PDB-7tmf: Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneum... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tmf | ||||||
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Title | Crystal Structure of NAD(P)H nitroreductase from Klebsiella pneumoniae (short b-axis) | ||||||
Components | NAD(P)H nitroreductase | ||||||
Keywords | OXIDOREDUCTASE / nitroreductase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | ||||||
Function / homology | Putative NAD(P)H nitroreductase YdjA-like / Nitroreductase / Nitroreductase family / Nitroreductase-like / Oxidoreductases / oxidoreductase activity / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Putative NAD(P)H nitroreductase Function and homology information | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2024 Title: Crystal structures of NAD(P)H nitroreductases from Klebsiella pneumoniae Authors: Kancherla, A.D. / Liu, L. / Tillery, L. / Shek, R. / Craig, J.K. / Machen, A.J. / Seibold, S. / Battaile, K.P. / Fradi, S. / Barrett, L.K. / Subramanian, S. / Myler, P. / Van Voorhis, W.C. / Lovell, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tmf.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmf.ent.gz | 66.3 KB | Display | PDB format |
PDBx/mmJSON format | 7tmf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmf ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmf | HTTPS FTP |
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-Related structure data
Related structure data | 7tmgC 3bm1S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21245.316 Da / Num. of mol.: 2 / Fragment: KlpnC.17456.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) Gene: ydjA, E3U37_20475, E3U38_02825, E9161_16570, NCTC9504_03979 Plasmid: KlpnC.17456.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A237MVZ9, Oxidoreductases |
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-Non-polymers , 6 types, 156 molecules
#2: Chemical | #3: Chemical | ChemComp-BTB / | #4: Chemical | #5: Chemical | ChemComp-PO4 / #6: Chemical | ChemComp-1PE / | #7: Water | ChemComp-HOH / | |
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-Details
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: 2.37 Å3/Da / Density % sol: 48.1 % / Mosaicity: 0.06 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Berkeley C1: 25 %w/v PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS-TRIS, KlpnC.17456.a.B1.PW39057 at 21 mg/mL, Tray: plate 12177 well C1 drop 1, Puck: PSL0413, Cryo: 80% crystallant and 20% PEG 200, |
-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: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→92.22 Å / Num. obs: 29253 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.042 / Rrim(I) all: 0.107 / Net I/σ(I): 12.4 / Num. measured all: 188186 / Scaling rejects: 59 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 3BM1 Resolution: 1.97→55.17 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / 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: 85.55 Å2 / Biso mean: 31.4906 Å2 / Biso min: 17.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.97→55.17 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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