- PDB-3do8: The crystal structure of the protein with unknown function from A... -
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Basic information
Entry
Database: PDB / ID: 3do8
Title
The crystal structure of the protein with unknown function from Archaeoglobus fulgidus
Components
Phosphopantetheine adenylyltransferase
Keywords
TRANSFERASE / Protein with unknown function / Archaeoglobus fulgidus / Structural genomics / MCSG / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / Coenzyme A biosynthesis / Cytoplasm / Nucleotidyltransferase
Function / homology
Function and homology information
pantetheine-phosphate adenylyltransferase / pantetheine-phosphate adenylyltransferase activity / coenzyme A biosynthetic process / ATP binding / cytoplasm Similarity search - Function
Resolution: 1.6→1.642 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.25 / Num. unique all: 2757 / % possible all: 86.87
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
HKL-3000
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.6→47.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.255 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.092 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.21372
1789
5 %
RANDOM
Rwork
0.16678
-
-
-
obs
0.16909
34228
96.23 %
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all
-
35569
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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: 18.06 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.12 Å2
0 Å2
-0.51 Å2
2-
-
-0.18 Å2
0 Å2
3-
-
-
1.09 Å2
Refinement step
Cycle: LAST / Resolution: 1.6→47.89 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2092
0
0
216
2308
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2126
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1557
X-RAY DIFFRACTION
r_angle_refined_deg
1.574
1.983
2851
X-RAY DIFFRACTION
r_angle_other_deg
0.988
3
3776
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.321
5
257
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.017
22.135
89
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.423
15
430
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.04
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
321
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
2272
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
437
X-RAY DIFFRACTION
r_nbd_refined
0.234
0.2
466
X-RAY DIFFRACTION
r_nbd_other
0.203
0.2
1675
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
1050
X-RAY DIFFRACTION
r_nbtor_other
0.08
0.2
1185
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.168
0.2
175
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.244
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.273
0.2
40
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.191
0.2
21
X-RAY DIFFRACTION
r_mcbond_it
1.917
1.5
1683
X-RAY DIFFRACTION
r_mcbond_other
0.821
1.5
525
X-RAY DIFFRACTION
r_mcangle_it
2.217
2
2088
X-RAY DIFFRACTION
r_scbond_it
3.767
3
976
X-RAY DIFFRACTION
r_scangle_it
5.055
4.5
763
LS refinement shell
Resolution: 1.6→1.642 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.266
114
-
Rwork
0.199
2281
-
obs
-
2395
86.87 %
Refinement TLS params.
Method: refined / Origin x: 8.898 Å / Origin y: 12.035 Å / Origin z: 34.019 Å
11
12
13
21
22
23
31
32
33
T
-0.0145 Å2
0.0107 Å2
-0.0138 Å2
-
-0.0174 Å2
0.003 Å2
-
-
-0.0411 Å2
L
0.9462 °2
-0.2316 °2
0.0078 °2
-
0.334 °2
0.0493 °2
-
-
0.064 °2
S
-0.0534 Å °
-0.0472 Å °
-0.0463 Å °
0.0223 Å °
0.0403 Å °
-0.0237 Å °
-0.0095 Å °
-0.0182 Å °
0.0131 Å °
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Label asym-ID
Auth seq-ID
Label seq-ID
1
X-RAY DIFFRACTION
1
A
A
1 - 141
1 - 141
2
X-RAY DIFFRACTION
1
B
B
2 - 124
2 - 124
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