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- PDB-7ldb: G150A Pseudomonas fluorescens isocyanide hydratase (G150A-3) at 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ldb | |||||||||
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Title | G150A Pseudomonas fluorescens isocyanide hydratase (G150A-3) at 274K, Phenix-refined | |||||||||
![]() | Isonitrile hydratase InhA | |||||||||
![]() | LYASE / DJ-1/PfpI superfamily | |||||||||
Function / homology | DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like / regulation of DNA-templated transcription / Isonitrile hydratase InhA![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Su, Z. / Dasgupta, M. / Yoon, C.H. / Wilson, M.A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. Authors: Su, Z. / Dasgupta, M. / Poitevin, F. / Mathews, I.I. / van den Bedem, H. / Wall, M.E. / Yoon, C.H. / Wilson, M.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.2 KB | Display | ![]() |
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PDB format | ![]() | 274.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.3 KB | Display | ![]() |
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Full document | ![]() | 439.7 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7l9qC ![]() 7l9sC ![]() 7l9wC ![]() 7l9zC ![]() 7la0C ![]() 7la3C ![]() 7lavC ![]() 7laxC ![]() 7lb9C ![]() 7lbhC ![]() 7lbiC ![]() 7lcxC ![]() 7ld6C ![]() 7ld7C ![]() 7ldiC ![]() 7ldmC ![]() 7ldoC ![]() 6ni5S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24194.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: inhA, PFL_4109 / Plasmid: pet15b / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6 Details: 25% PEG 3350, 200 MM MAGNESIUM CHLORIDE, 100MM TRIS-HCL, PH 8.6, 2 MM Dithiothreitol |
-Data collection
Diffraction | Mean temperature: 274 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2018 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.775 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→39.17 Å / Num. obs: 85576 / % possible obs: 93 % / Redundancy: 2.1 % / Biso Wilson estimate: 14.22 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.064 / Net I/σ(I): 6 |
Reflection shell | Resolution: 1.35→1.38 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4083 / CC1/2: 0.264 / Rrim(I) all: 1.384 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6NI5 Resolution: 1.35→34.63 Å / SU ML: 0.1244 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.7224 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→34.63 Å
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Refine LS restraints |
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LS refinement shell |
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