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- PDB-4brh: Legionella pneumophila NTPDase1 crystal form II (closed) in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4brh | |||||||||
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Title | Legionella pneumophila NTPDase1 crystal form II (closed) in complex with MG AND THIAMINE PHOSPHOVANADATE | |||||||||
![]() | ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I | |||||||||
![]() | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Zebisch, M. / Schaefer, P. / Lauble, P. / Straeter, N. | |||||||||
![]() | ![]() Title: Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases. Authors: Zebisch, M. / Krauss, M. / Schafer, P. / Lauble, P. / Strater, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 263.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4bqzC ![]() 4br0C ![]() 4br2C ![]() 4br4C ![]() 4br5C ![]() 4br7C ![]() 4br9C ![]() 4braC ![]() 4brcC ![]() 4brdC ![]() 4breC ![]() 4brfC ![]() 4brgC ![]() 4briC ![]() 4brkC ![]() 4brlC ![]() 4brmC ![]() 4brnC ![]() 4broC ![]() 4brpC ![]() 4brqC C: citing same article ( |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.413, 0.068, -0.908), Vector ![]() |
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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.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 445 molecules ![](data/chem/img/TMV.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/DVT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/DVT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | ![]() #7: Chemical | ChemComp-GOL / | ![]() #8: Water | ChemComp-HOH / | ![]() |
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-Details
Nonpolymer details | 2-(N-MORPHOLINO)ETHANESULFONIC ACID (MES): PH BUFFER MES THIAMINE-PHOSPHOVANADATE (TMV): TRANSITION ...2-(N-MORPHOLINO |
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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 % / Description: NONE |
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Crystal grow![]() | pH: 5.6 / Details: 100MM NAMES PH 5.6, 11% PEG3350, 20MM MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.69→29 Å / Num. obs: 80289 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 34.3 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure![]() Starting model: NONE Resolution: 1.69→29.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.084 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
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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: 18.783 Å2
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Refinement step | Cycle: LAST / Resolution: 1.69→29.04 Å
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Refine LS restraints |
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