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Yorodumi- PDB-4brf: Legionella pneumophila NTPDase1 crystal form II (closed) in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4brf | ||||||
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Title | Legionella pneumophila NTPDase1 crystal form II (closed) in complex with a distorted orthomolybdate ion and AMP | ||||||
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 / OTHER / Resolution: 1.6 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 | 4brf.cif.gz | 335.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4brf.ent.gz | 281.6 KB | Display | PDB format |
PDBx/mmJSON format | 4brf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/4brf ftp://data.pdbj.org/pub/pdb/validation_reports/br/4brf | HTTPS FTP |
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-Related structure data
Related structure data | 4bqzC 4br0C 4br2C 4br4C 4br5C 4br7C 4br9C 4braC 4brcC 4brdC 4breC 4brgC 4brhC 4briC 4brkC 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: (0.406, 0.075, -0.911), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 41880.594 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-393 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 , 10 types, 565 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Chemical | ChemComp-M27 / | #8: Chemical | ChemComp-EDO / | #9: Chemical | #10: Chemical | ChemComp-AMP / | #11: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES ORTHO MOLYBDATE (MOO): DISTORTED MOLYBDATE ...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 NA+ MES PH 5.4, 100MM NACL, 14% PEG3350, 20MM MGCL2, 50MM MGSO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 93825 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4 |
-Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.6→29.87 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.639 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.08 / 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: 23.786 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.87 Å
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