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Yorodumi- PDB-7ri0: Aspergillus fumigatus Enolase Bound to Phosphoenolpyruvate and 2-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ri0 | ||||||
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Title | Aspergillus fumigatus Enolase Bound to Phosphoenolpyruvate and 2-Phosphoglycerate | ||||||
Components | Enolase | ||||||
Keywords | LYASE / glycolysis | ||||||
Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / IgE binding / glycolytic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Nguyen, S. / Bruning, J.B. | ||||||
Citation | Journal: Proteins / Year: 2022 Title: A structural model of the human plasminogen and Aspergillus fumigatus enolase complex. Authors: Nguyen, S. / Jovcevski, B. / Truong, J.Q. / Pukala, T.L. / Bruning, J.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ri0.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ri0.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ri0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/7ri0 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/7ri0 | HTTPS FTP |
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-Related structure data
Related structure data | 7rhvSC 7rhwC 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
#1: Protein | Mass: 48537.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: enoA, AFUA_6G06770 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96X30, phosphopyruvate hydratase #2: Chemical | #3: Chemical | ChemComp-2PG / | #4: Chemical | ChemComp-PEP / | #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: 2.47 Å3/Da / Density % sol: 50.26 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 21% PEG 3350, 0.05 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 30, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→46.9 Å / Num. obs: 42138 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Net I/σ(I): 13.3 / Num. measured all: 302573 / Scaling rejects: 64 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7RHV Resolution: 2.3→42.497 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.04 / 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: 81.27 Å2 / Biso mean: 24.1257 Å2 / Biso min: 7.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→42.497 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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