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- PDB-5a68: Crystal structure of the AtTTM3 product complex with two orthopho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a68 | ||||||
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Title | Crystal structure of the AtTTM3 product complex with two orthophosphates and manganese ions (form B) | ||||||
![]() | TRIPHOSPHATE TUNEL METALLOENZYME 3 | ||||||
![]() | HYDROLASE / INORGANIC POLYPHOSPHATE / TRIPOLYPHOSPHATE / TRIPHOSPHATE TUNNEL METALLOENZYME | ||||||
Function / homology | ![]() triphosphatase / inorganic triphosphate phosphatase activity / root development / anaphase-promoting complex / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
![]() | ![]() Title: Structural Determinants for Substrate Binding and Catalysis in Triphosphate Tunnel Metalloenzymes. Authors: Martinez, J. / Truffault, V. / Hothorn, M. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 80.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 434.4 KB | Display | |
Data in XML | ![]() | 10.7 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a5yC ![]() 5a60C ![]() 5a61C ![]() 5a64C ![]() 5a65C ![]() 5a66C ![]() 5a67C 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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Components
#1: Protein | Mass: 24323.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.96 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.1 M BIS TRIS PH 7.0, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99998 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→43.2 Å / Num. obs: 23035 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.67→1.77 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.75 / % possible all: 76.8 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.67→43.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.345 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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: 29.197 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→43.2 Å
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Refine LS restraints |
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