- PDB-1z9t: CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA C... -
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Basic information
Entry
Database: PDB / ID: 1z9t
Title
CRYSTAL STRUCTURE OF A PUTATIVE LACCASE (YFIH) FROM ESCHERICHIA COLI AT 1.54 A RESOLUTION
Components
Hypothetical UPF0124 protein yfiH
Keywords
OXIDOREDUCTASE / PUTATIVE LACCASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information
Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor / 2'-deoxyadenosine deaminase activity / adenosine deaminase / S-methyl-5'-thioadenosine phosphorylase / adenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / peptidoglycan metabolic process / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / outer membrane-bounded periplasmic space / copper ion binding / protein homodimerization activity / cytosol Similarity search - Function
Resolution: 1.54→60.3 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.087 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MASS SPEC ANALYSIS SHOWED THAT THE SE-METHIONINE INCORPATION RATE WAS ONLY 63% AND THE MODEL IS BUILT WITH THE OCCUPANCY OF THE SE ATOMS IN ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MASS SPEC ANALYSIS SHOWED THAT THE SE-METHIONINE INCORPATION RATE WAS ONLY 63% AND THE MODEL IS BUILT WITH THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES AT 0.75 OCCUPANCY TO ACCOUNT FOR THE REDUCED SCATTERING POWER FROM THE 37% S-MET RESIDUES
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.172
2262
5 %
RANDOM
Rwork
0.142
-
-
-
all
0.143
-
-
-
obs
0.14324
42591
99.95 %
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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: 17.354 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.57 Å2
0 Å2
0 Å2
2-
-
-0.57 Å2
0 Å2
3-
-
-
1.13 Å2
Refinement step
Cycle: LAST / Resolution: 1.54→60.3 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1799
0
102
218
2119
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1935
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1767
X-RAY DIFFRACTION
r_angle_refined_deg
1.732
1.973
2597
X-RAY DIFFRACTION
r_angle_other_deg
1.447
3
4077
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.88
5
238
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.249
23.375
80
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.755
15
274
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.24
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.098
0.2
279
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.02
2138
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
390
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
366
X-RAY DIFFRACTION
r_nbd_other
0.189
0.2
1801
X-RAY DIFFRACTION
r_nbtor_refined
0.179
0.2
945
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
1109
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.143
0.2
159
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.142
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.238
0.2
36
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.238
0.2
22
X-RAY DIFFRACTION
r_mcbond_it
2.004
3
1261
X-RAY DIFFRACTION
r_mcbond_other
0.474
3
491
X-RAY DIFFRACTION
r_mcangle_it
2.437
5
1901
X-RAY DIFFRACTION
r_scbond_it
4.358
8
816
X-RAY DIFFRACTION
r_scangle_it
6.193
11
695
LS refinement shell
Resolution: 1.54→1.58 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.232
178
-
Rwork
0.209
3082
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obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: -11.7438 Å / Origin y: 20.0477 Å / Origin z: 2.7803 Å
11
12
13
21
22
23
31
32
33
T
-0.0599 Å2
-0.0136 Å2
0.0089 Å2
-
-0.0317 Å2
-0.0228 Å2
-
-
-0.008 Å2
L
1.0029 °2
-0.3494 °2
-0.3517 °2
-
0.4629 °2
0.2194 °2
-
-
0.6086 °2
S
-0.0343 Å °
0.0688 Å °
-0.001 Å °
-0.0294 Å °
-0.0136 Å °
0.02 Å °
-0.0013 Å °
-0.0449 Å °
0.0478 Å °
Refinement TLS group
Selection: ALL
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