- PDB-3djc: CRYSTAL STRUCTURE OF PANTOTHENATE KINASE FROM LEGIONELLA PNEUMOPHILA -
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Basic information
Entry
Database: PDB / ID: 3djc
Title
CRYSTAL STRUCTURE OF PANTOTHENATE KINASE FROM LEGIONELLA PNEUMOPHILA
Components
Type III pantothenate kinase
Keywords
TRANSFERASE / STRUCTURAL GENOMICS / PANTOTHENATE KINASE / PUTATIVE TRANSFERASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / ATP-binding / Coenzyme A biosynthesis / Kinase / Metal-binding / Nucleotide-binding / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information
pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / metal ion binding / cytoplasm Similarity search - Function
Type III pantothenate kinase / Type III pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
A: Type III pantothenate kinase B: Type III pantothenate kinase C: Type III pantothenate kinase D: Type III pantothenate kinase E: Type III pantothenate kinase F: Type III pantothenate kinase G: Type III pantothenate kinase H: Type III pantothenate kinase I: Type III pantothenate kinase J: Type III pantothenate kinase K: Type III pantothenate kinase L: Type III pantothenate kinase hetero molecules
G: Type III pantothenate kinase H: Type III pantothenate kinase I: Type III pantothenate kinase J: Type III pantothenate kinase K: Type III pantothenate kinase L: Type III pantothenate kinase hetero molecules
A: Type III pantothenate kinase B: Type III pantothenate kinase C: Type III pantothenate kinase D: Type III pantothenate kinase E: Type III pantothenate kinase F: Type III pantothenate kinase hetero molecules
Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 15, 2007
Radiation
Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97969 Å / Relative weight: 1
Reflection
Resolution: 2.35→50 Å / Num. obs: 140651 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 62.35 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 3
Reflection shell
Resolution: 2.35→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 0.4 / Rsym value: 0.833 / % possible all: 94.9
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Processing
Software
Name
Version
Classification
SHELXD
phasing
REFMAC
5.2.0019
refinement
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: SAD / Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.87 / SU B: 12.224 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.313
3908
3 %
RANDOM
Rwork
0.259
-
-
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obs
0.261
124742
97.5 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parameters
Biso mean: 63.24 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.05 Å2
0 Å2
-0.48 Å2
2-
-
0.17 Å2
0 Å2
3-
-
-
-0.18 Å2
Refinement step
Cycle: LAST / Resolution: 2.4→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
23182
0
66
285
23533
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
23996
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.245
1.966
32542
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.843
5
3140
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.654
23.856
975
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.33
15
4182
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.158
15
143
X-RAY DIFFRACTION
r_chiral_restr
0.085
0.2
3860
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
17685
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.13
0.3
10346
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.297
0.5
16096
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.169
0.5
1226
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.092
0.3
78
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.215
0.5
10
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
6.433
3
15655
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
8.698
4
24606
X-RAY DIFFRACTION
r_scbond_it
11.242
5
9218
X-RAY DIFFRACTION
r_scangle_it
13.94
7
7878
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.4→2.46 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.399
224
-
Rwork
0.282
7552
-
obs
-
-
80.87 %
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