Crystal structure of 3-oxoacyl-(acyl carrier protein) reductase (TM1169) from Thermotoga maritima at 2.50 A resolution
Components
3-oxoacyl-(acyl carrier protein) reductase
Keywords
OXIDOREDUCTASE / TM1169 / 3-OXOACYL-(ACYL CARRIER PROTEIN) REDUCTASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information
oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / antibiotic biosynthetic process / NADP binding Similarity search - Function
Resolution: 2.5→41.17 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.212 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 1.807 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER ...Details: 1. HYDROGENS HAVE BEEN ADDED TO THE RIDING POSITIONS. 2. NAD WAS FITTED IN SUBUNIT B BASED ON WEAK ELECTRON DENSITY CORRESPONDING TO THE NAD LOCATION IN THE HOMOLOG (1FMC). IN THE OTHER SUBUNITS, ELECTRON DENSITY IS SUGGESTIVE BUT TOO WEAKTO JUSTIFY FITTING NAD, PRESUMABLY DUE TO DIFFERING CRYSTAL CONTACTS. 3. THE DISULFIDE BOND (37-54) HAS NEGATIVE DIFFERENCE DENSITY IN ALL SUBUNITS, PRESUMABLY DUE TO RADIATION DAMAGE. 4. NCS IS BROKEN AT RESIDUES 54-61 AND 84/137, DUE TO CRYSTAL CONTACTS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2468
1562
4.9 %
RANDOM
Rwork
0.19404
-
-
-
obs
0.19662
30035
85.03 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 15.52 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.87 Å2
0 Å2
0 Å2
2-
-
-6.16 Å2
0 Å2
3-
-
-
8.03 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→41.17 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
7165
0
35
161
7361
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
7310
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
6956
X-RAY DIFFRACTION
r_angle_refined_deg
1.755
1.978
9890
X-RAY DIFFRACTION
r_angle_other_deg
0.944
3
16116
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.747
5
932
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.365
23.916
286
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.263
15
1311
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.795
15
51
X-RAY DIFFRACTION
r_chiral_restr
0.095
0.2
1165
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
8033
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
1432
X-RAY DIFFRACTION
r_nbd_refined
0.204
0.2
1602
X-RAY DIFFRACTION
r_nbd_other
0.189
0.2
7081
X-RAY DIFFRACTION
r_nbtor_other
0.089
0.2
4713
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.031
0.2
3
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.241
0.2
22
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.312
0.2
61
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.487
0.2
3
X-RAY DIFFRACTION
r_mcbond_it
0.705
1.5
4752
X-RAY DIFFRACTION
r_mcangle_it
1.216
2
7474
X-RAY DIFFRACTION
r_scbond_it
1.648
3
2868
X-RAY DIFFRACTION
r_scangle_it
2.774
4.5
2416
Refine LS restraints NCS
Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
A
1319
tightpositional
0.06
0.05
2
B
1319
tightpositional
0.06
0.05
3
C
1319
tightpositional
0.06
0.05
4
D
1319
tightpositional
0.05
0.05
1
A
2000
loosepositional
0.52
5
2
B
2000
loosepositional
0.48
5
3
C
2000
loosepositional
0.59
5
4
D
2000
loosepositional
0.54
5
1
A
1319
tightthermal
1.67
10
2
B
1319
tightthermal
1.96
10
3
C
1319
tightthermal
2.31
10
4
D
1319
tightthermal
2.13
10
1
A
2000
loosethermal
1.85
10
2
B
2000
loosethermal
2.16
10
3
C
2000
loosethermal
2.52
10
4
D
2000
loosethermal
2.39
10
LS refinement shell
Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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