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Yorodumi- PDB-8afv: DaArgC3 - Engineered Formyl Phosphate Reductase with 3 substituti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8afv | |||||||||
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Title | DaArgC3 - Engineered Formyl Phosphate Reductase with 3 substitutions (S178V, G182V, L233I) | |||||||||
Components | N-acetyl-gamma-glutamyl-phosphate reductase | |||||||||
Keywords | OXIDOREDUCTASE / formyl phosphate | |||||||||
Function / homology | Function and homology information N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / arginine biosynthetic process / NADP+ binding / NAD binding / protein dimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Denitrovibrio acetiphilus DSM 12809 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | |||||||||
Authors | Pfister, P. / Nattermann, M. / Zarzycki, J. / Erb, T.J. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: To Be Published Title: N-acetyl-gamma-glutamyl-phosphate reductase of Denitrovibrio acetiphilus Authors: Nattermann, M. / Wenk, S. / Pfister, P. / Guntermann, N. / Nickel, L. / Zarzycki, J. / Francio, G. / Leitner, W. / Bar-Even, A. / Erb, T.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8afv.cif.gz | 521.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8afv.ent.gz | 430.8 KB | Display | PDB format |
PDBx/mmJSON format | 8afv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/8afv ftp://data.pdbj.org/pub/pdb/validation_reports/af/8afv | HTTPS FTP |
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-Related structure data
Related structure data | 3dr3S 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: 38001.469 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Denitrovibrio acetiphilus DSM 12809 (bacteria) Strain: DSM 12809 / NBRC 114555 / N2460 / Gene: argC, Dacet_0460 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: D4H3H4, N-acetyl-gamma-glutamyl-phosphate reductase #2: Chemical | ChemComp-NA / #3: 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: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Sodium chloride 0.1 M HEPES pH 7.5 25%(w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: cryostream / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.19→42.364 Å / Num. obs: 66917 / % possible obs: 97 % / Redundancy: 3.2 % / Biso Wilson estimate: 29.75 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.068 / Rsym value: 0.057 / Net I/av σ(I): 8.8 / Net I/σ(I): 13.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3dr3 Resolution: 2.19→42.36 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / 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: 134.56 Å2 / Biso mean: 38.5589 Å2 / Biso min: 14.74 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.19→42.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: -38.4898 Å / Origin y: -1.2472 Å / Origin z: -0.0408 Å
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Refinement TLS group |
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