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Yorodumi- PDB-7tmd: Crystal structure of Ornithine carbamoyltransferase from Klebsiel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tmd | ||||||
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Title | Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae | ||||||
Components | Ornithine carbamoyltransferaseOrnithine transcarbamylase | ||||||
Keywords | TRANSFERASE / Ornithine carbamoyltransferase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | ||||||
Function / homology | Function and homology information ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / amino acid binding / cytoplasm Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To be published Title: Crystal structure of Ornithine carbamoyltransferase from Klebsiella pneumoniae Authors: Lovell, S. / Liu, L. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tmd.cif.gz | 381.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tmd.ent.gz | 310.7 KB | Display | PDB format |
PDBx/mmJSON format | 7tmd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/7tmd ftp://data.pdbj.org/pub/pdb/validation_reports/tm/7tmd | HTTPS FTP |
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-Related structure data
Related structure data | 1duvS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37577.824 Da / Num. of mol.: 6 / Fragment: KlpnC.00088.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria) Strain: HS11286 / Gene: KPHS_05120 / Plasmid: KlpnC.00088.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3GHJ1, ornithine carbamoyltransferase #2: Chemical | ChemComp-IOD / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.46 Å3/Da / Density % sol: 49.91 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus B10: 12% (v/v) Ethylene glycol: 6 % (w/v) PEG 8000, 0.1 M (Sodium HEPES: MOPS (acid)), 0.03M Sodium fluoride: 0.03M Sodium bromide: 0.03M Sodium iodide: KlpnC.00088.a.B1.PS38685 at ...Details: Morpheus B10: 12% (v/v) Ethylene glycol: 6 % (w/v) PEG 8000, 0.1 M (Sodium HEPES: MOPS (acid)), 0.03M Sodium fluoride: 0.03M Sodium bromide: 0.03M Sodium iodide: KlpnC.00088.a.B1.PS38685 at 24.8 mg/mL, Tray: plate 12314 well B10 drop 1, Puck: PSL1108, 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: 0.9795 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 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: 2.35→48.79 Å / Num. obs: 88612 / % possible obs: 98.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.4 / Num. measured all: 312992 / Scaling rejects: 343 | ||||||||||||||||||||||||
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: 1DUV Resolution: 2.35→47.54 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 24.86 / 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: 125.81 Å2 / Biso mean: 35.0523 Å2 / Biso min: 12.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→47.54 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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