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Yorodumi- PDB-4dyw: Crystal structure of MutT NUDIX hydrolase from Burkholderia pseud... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyw | ||||||
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Title | Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei | ||||||
Components | MutT/NUDIX family protein | ||||||
Keywords | HYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / MutT / NUDIX hydrolase / nucleotide diphosphate X hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Burkholderia pseudomallei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei Authors: Edwards, T.E. / Clifton, M.C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dyw.cif.gz | 112 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyw.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 4dyw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyw ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyw | HTTPS FTP |
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-Related structure data
Related structure data | 3hhjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 5 - 133 / Label seq-ID: 26 - 154
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-Components
#1: Protein | Mass: 17335.723 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_0547 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JWU2 #2: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: BupsA.00264.a.A1 PS01261 at 27 mg/mL against 0.2 M NaK Tartrate, 30% PEG 3350 PACT E9 focus screen with 20% ethylene glycol as cro-protectant, crystal tracking ID 230892e11, pH 7.0, VAPOR ...Details: BupsA.00264.a.A1 PS01261 at 27 mg/mL against 0.2 M NaK Tartrate, 30% PEG 3350 PACT E9 focus screen with 20% ethylene glycol as cro-protectant, crystal tracking ID 230892e11, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976484 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976484 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. all: 12763 / Num. obs: 12669 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 51.427 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.52 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3HHJ Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1804 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8144 / SU B: 17.4 / SU ML: 0.189 / SU R Cruickshank DPI: 0.374 / SU Rfree: 0.2609 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.374 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.6 Å2 / Biso mean: 45.9818 Å2 / Biso min: 24.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | T23: -0.0179 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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