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Yorodumi- PDB-8doq: Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate en... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8doq | |||||||||
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Title | Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P21 Form) | |||||||||
Components | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase | |||||||||
Keywords | ISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | |||||||||
Function / homology | Function and homology information orotidine-5'-phosphate decarboxylase / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process Similarity search - Function | |||||||||
Biological species | Klebsiella aerogenes (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from Klebsiella aerogenes (P1 Form) Authors: Liu, L. / Seibold, S. / Battaile, K.P. / Lovell, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8doq.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8doq.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 8doq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/8doq ftp://data.pdbj.org/pub/pdb/validation_reports/do/8doq | HTTPS FTP |
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-Related structure data
Related structure data | 8dopSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27335.434 Da / Num. of mol.: 2 / Fragment: KlaeA.01229.a.B1 / Mutation: D42E, T152M, A182V, A239V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella aerogenes (bacteria) / Gene: pyrF, BXQ27_18035, HV316_11080, KCTC 2190 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0M3H420, orotidine-5'-phosphate decarboxylase #2: Chemical | ChemComp-BEZ / | #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: 2.13 Å3/Da / Density % sol: 42.16 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: ...Details: Morpheus A4: 12.5%(v/v) MPD, 12.5%(v/v) PEG 1000, 12.5%(w/v) PEG 3350, 100 mM Imidazole/MES, 30 mM MgCl2 and 30 mM CaCl2, KlaeA.01229.a.B1 at 15 mg/mL, Tray: plate 12527 well A4 drop 1, Puck: PSL0809, Cryo: DIRECT; Electron density consistent with a benzoic acid molecule was observed and modeled. The source of this is unknown and it may have been acquired from the expression host |
-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: Apr 8, 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: 1.65→70.5 Å / Num. obs: 55090 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.81 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.058 / Rrim(I) all: 0.111 / Net I/σ(I): 6.4 / Num. measured all: 194613 / Scaling rejects: 181 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.6 %
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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: 8DOP Resolution: 1.65→39.4 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.18 Å2 / Biso mean: 26.6252 Å2 / Biso min: 9.69 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→39.4 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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