+Open data
-Basic information
Entry | Database: PDB / ID: 5hp7 | ||||||||||||
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Title | Crystal structures of RidA in the apo form | ||||||||||||
Components | Reactive Intermediate Deaminase A, chloroplastic | ||||||||||||
Keywords | HYDROLASE / RidA / enamine/imine / deamination | ||||||||||||
Function / homology | Function and homology information 2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / organonitrogen compound catabolic process / deaminase activity / branched-chain amino acid biosynthetic process / plant-type vacuole / chloroplast envelope / thylakoid / isoleucine biosynthetic process ...2-iminobutanoate deaminase activity / 2-iminopropanoate deaminase activity / 2-iminobutanoate/2-iminopropanoate deaminase / organonitrogen compound catabolic process / deaminase activity / branched-chain amino acid biosynthetic process / plant-type vacuole / chloroplast envelope / thylakoid / isoleucine biosynthetic process / plastid / chloroplast stroma / chloroplast / response to toxic substance / cytosol Similarity search - Function | ||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Xie, W. / Liu, X. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structures of RidA, an important enzyme for the prevention of toxic side products Authors: Liu, X. / Zeng, J. / Chen, X. / Xie, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hp7.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hp7.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 5hp7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/5hp7 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hp7 | HTTPS FTP |
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-Related structure data
Related structure data | 5hp8C 2b33S C: citing same article (ref.) S: Starting model for refinement |
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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: 13231.139 Da / Num. of mol.: 1 / Fragment: UNP residues 68-187 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RIDA, At3g20390, MQC12.15 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) References: UniProt: Q94JQ4, 2-iminobutanoate/2-iminopropanoate deaminase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 29.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 18% PEG 3350, 0.1 M MES pH6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.7 Å / Num. obs: 6001 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 5.5 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B33 Resolution: 2→25.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.068 / SU ML: 0.111 / Cross valid method: FREE R-VALUE / ESU R: 0.2 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.532 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.67 Å
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Refine LS restraints |
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