- PDB-1o50: Crystal structure of a cbs domain-containing protein (tm0935) fro... -
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Basic information
Entry
Database: PDB / ID: 1o50
Title
Crystal structure of a cbs domain-containing protein (tm0935) from thermotoga maritima at 1.87 A resolution
Components
CBS domain-containing predicted protein TM0935
Keywords
TRANSFERASE / Cbs-domain pair fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological species
Thermotoga maritima (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
Method to determine structure: MAD / Resolution: 1.87→31.43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.887 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. ADDITIONAL N-TERMINAL HIS-TAG RESIDUES INDICATED BY CONTINUOUS BUT UNINTERPRETABLE DENSITY, AND WAS MODELED BY WATERS. 2. PROMINENT DENSITY AT MISSING RESIDUE A70 WAS MODELED AS WATER ...Details: 1. ADDITIONAL N-TERMINAL HIS-TAG RESIDUES INDICATED BY CONTINUOUS BUT UNINTERPRETABLE DENSITY, AND WAS MODELED BY WATERS. 2. PROMINENT DENSITY AT MISSING RESIDUE A70 WAS MODELED AS WATER CHAIN. 3. PROMINENT CONTINUOUS DENSITY AROUND RESIDUE A29 WAS MODELED AS WATER CHAIN. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25495
813
5.1 %
RANDOM
Rwork
0.19113
-
-
-
obs
0.19435
15161
99.41 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 32.331 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.17 Å2
0 Å2
0 Å2
2-
-
-0.17 Å2
0 Å2
3-
-
-
0.34 Å2
Refinement step
Cycle: LAST / Resolution: 1.87→31.43 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1124
0
0
214
1338
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.018
0.022
1153
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1108
X-RAY DIFFRACTION
r_angle_refined_deg
1.549
1.984
1558
X-RAY DIFFRACTION
r_angle_other_deg
0.882
3
2592
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.331
5
139
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.217
25.625
48
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.825
15
228
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
8.069
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.1
0.2
186
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1219
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
192
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
235
X-RAY DIFFRACTION
r_nbd_other
0.233
0.2
1271
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
658
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.222
0.2
134
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.106
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.253
0.2
54
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.115
0.2
16
X-RAY DIFFRACTION
r_mcbond_it
0.799
1.5
708
X-RAY DIFFRACTION
r_mcangle_it
1.372
2
1163
X-RAY DIFFRACTION
r_scbond_it
2.123
3
445
X-RAY DIFFRACTION
r_scangle_it
3.409
4.5
395
LS refinement shell
Resolution: 1.87→1.919 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.372
65
5.73 %
Rwork
0.339
1069
-
Refinement TLS params.
Method: refined / Origin x: 19.361 Å / Origin y: 6.083 Å / Origin z: 90.821 Å
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