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- PDB-1w7w: Structure and mutational analysis of a plant mitochondrial nucleo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w7w | ||||||
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Title | Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase: identification of residues involved in serine phosphorylation and oligomerization. | ||||||
![]() | NUCLEOSIDE DIPHOSPHATE KINASE | ||||||
![]() | TRANSFERASE / MITOCHONDRIAL NUCLEOSIDE DIPHOSPHATE KINASE / NDPK3 / PISUM SATIVUM / KINASE | ||||||
Function / homology | ![]() nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Johansson, M. / MacKenzie-Hose, A. / Andersson, I. / Knorpp, C. | ||||||
![]() | ![]() Title: Structure and Mutational Analysis of a Plant Mitochondrial Nucleoside Diphosphate Kinase: Identification of Residues Involved in Serine Phosphorylation and Oligomerisation Authors: Johansson, M. / Mackenzie-Hose, A. / Andersson, I. / Knorpp, C. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.1 KB | Display | ![]() |
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PDB format | ![]() | 146.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.2 KB | Display | ![]() |
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Full document | ![]() | 496 KB | Display | |
Data in XML | ![]() | 34.9 KB | Display | |
Data in CIF | ![]() | 46.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f6tS S: Starting model for refinement |
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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:
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Components
#1: Protein | Mass: 20722.404 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | pH: 5.5 Details: 16 TO 18% METHYL PENTANEDIOL, 100 MM SODIUM ACETATE, PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 14, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 26099 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 5.46 % / Biso Wilson estimate: 50.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.7 / % possible all: 85.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1F6T Resolution: 2.8→19.84 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2021609.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 20.122 Å2 / ksol: 0.307388 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→19.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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