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Yorodumi- PDB-4brk: Legionella pneumophila NTPDase1 N302Y variant crystal form III (c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4brk | ||||||
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Title | Legionella pneumophila NTPDase1 N302Y variant crystal form III (closed) in complex with MG UMPPNP | ||||||
Components | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I | ||||||
Keywords | HYDROLASE / APYRASE / ATPASE / ADPASE / CD39 / PURINERGIC SIGNALLING / DOMAIN ROTATION / TRANSITION STATE / NTPDASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | LEGIONELLA PNEUMOPHILA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å | ||||||
Authors | Zebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N. | ||||||
Citation | Journal: Structure / Year: 2013 Title: Crystallographic Snapshots Along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases Authors: Zebisch, M. / Krauss, M. / Schaefer, P. / Lauble, P. / Straeter, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4brk.cif.gz | 338.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4brk.ent.gz | 284.2 KB | Display | PDB format |
PDBx/mmJSON format | 4brk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4brk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4brk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4brk_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 4brk_validation.cif.gz | 56.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/4brk ftp://data.pdbj.org/pub/pdb/validation_reports/br/4brk | HTTPS FTP |
-Related structure data
Related structure data | 4bqzC 4br0C 4br2C 4br4C 4br5C 4br7C 4br9C 4braC 4brcC 4brdC 4breC 4brfC 4brgC 4brhC 4briC 4brlC 4brmC 4brnC 4broC 4brpC 4brqC C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.985, 0.063, 0.158), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41929.664 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-393 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEGIONELLA PNEUMOPHILA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5ZUA2, apyrase |
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-Non-polymers , 6 types, 777 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES PHOSPHOAMINOPHOSPHONIC ACID-URIDYLATE ...2-(N-MORPHOLINO |
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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 5.4 Details: 100MM NAMES PH 5.4, 10% PEG3350, 15% GLYCEROL, 10MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.8943 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8943 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→28 Å / Num. obs: 117553 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.5→27.43 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.403 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.928 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.43 Å
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