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Yorodumi- PDB-3exq: Crystal structure of a NUDIX family hydrolase from Lactobacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3exq | ||||||
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Title | Crystal structure of a NUDIX family hydrolase from Lactobacillus brevis | ||||||
Components | NUDIX family hydrolase | ||||||
Keywords | HYDROLASE / NUDIX / Protein Structure Initiative II(PSI II) / NYSGXRC / 11180k / Structural Genomics / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Lactobacillus brevis ATCC 367 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Palani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a NUDIX family hydrolase from Lactobacillus brevis Authors: Palani, K. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3exq.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3exq.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 3exq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3exq_validation.pdf.gz | 435.8 KB | Display | wwPDB validaton report |
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Full document | 3exq_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 3exq_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3exq_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/3exq ftp://data.pdbj.org/pub/pdb/validation_reports/ex/3exq | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17986.666 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus brevis ATCC 367 (bacteria) Gene: LVIS_0842 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03S37 | ||
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#2: Chemical | #3: 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: 2.76 Å3/Da / Density % sol: 55.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Sodium chloride, 0.1M HEPES, 1.6M Ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 10, 2008 / Details: Mirrors |
Radiation | Monochromator: Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.1 Å / Num. all: 14576 / Num. obs: 14576 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 13 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.98→2.05 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.226 / Mean I/σ(I) obs: 3 / Num. unique all: 1418 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→35.09 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 145595.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4253 Å2 / ksol: 0.366071 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→35.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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