nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / metal ion binding Similarity search - Function
Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.1 Å3/Da / Density % sol: 42.5 % Description: THE STARTING MODEL WAS PREVIOUS LITOPENAEUS VANNAMEI NDK STRUCTURE COMPLEXED WITH DADP WHICH WILL BE DEPOSITED IN PDB
Crystal grow
pH: 8.5 Details: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.1 M TRIS-HCL PH 8.5 AND 30% (W/V) PEG 4,000
Monochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 2→34.8 Å / Num. obs: 29462 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.7
Reflection shell
Resolution: 2→2.1 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.4 / % possible all: 96.4
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Processing
Software
Name
Version
Classification
PHENIX
(PHENIX.REFINE: 1.8.2_1309)
refinement
HKL-2000
datareduction
SCALEPACK
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT Starting model: SHRIMP NDK STRUCTURE TO BE DEPOSITED Resolution: 2.007→34.887 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 24.19 / Stereochemistry target values: ML Details: NO ELECTRON DENSITY WAS FOUND FOR ADP IN THE CHAIN A ACTIVE SITE. ALSO NUCLEOTIDE BINDING LOOP IN CHAIN A THAT COMPRISE RESIDUES 44-66 WERE DISORDERED. THEREFORE, BOTH LIGAND AND DISORDERED ...Details: NO ELECTRON DENSITY WAS FOUND FOR ADP IN THE CHAIN A ACTIVE SITE. ALSO NUCLEOTIDE BINDING LOOP IN CHAIN A THAT COMPRISE RESIDUES 44-66 WERE DISORDERED. THEREFORE, BOTH LIGAND AND DISORDERED LOOP WERE NOT INCLUDED IN IN FINAL THE MODEL.
Rfactor
Num. reflection
% reflection
Rfree
0.217
1497
5.1 %
Rwork
0.178
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-
obs
0.18
29447
99.58 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 2.007→34.887 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3371
0
56
419
3846
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
3493
X-RAY DIFFRACTION
f_angle_d
1.169
4720
X-RAY DIFFRACTION
f_dihedral_angle_d
14.657
1302
X-RAY DIFFRACTION
f_chiral_restr
0.081
503
X-RAY DIFFRACTION
f_plane_restr
0.004
594
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.0072-2.0719
0.2987
128
0.2411
2423
X-RAY DIFFRACTION
96
2.0719-2.146
0.2755
131
0.2079
2510
X-RAY DIFFRACTION
100
2.146-2.2319
0.2225
127
0.1941
2524
X-RAY DIFFRACTION
100
2.2319-2.3334
0.2522
130
0.1993
2538
X-RAY DIFFRACTION
100
2.3334-2.4564
0.2415
134
0.1906
2513
X-RAY DIFFRACTION
100
2.4564-2.6103
0.2478
124
0.1904
2543
X-RAY DIFFRACTION
100
2.6103-2.8117
0.2431
143
0.1903
2533
X-RAY DIFFRACTION
100
2.8117-3.0945
0.2335
153
0.1767
2525
X-RAY DIFFRACTION
100
3.0945-3.542
0.2201
119
0.1614
2602
X-RAY DIFFRACTION
100
3.542-4.461
0.1704
152
0.1537
2569
X-RAY DIFFRACTION
100
4.461-34.8925
0.1951
156
0.1712
2670
X-RAY DIFFRACTION
100
+
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