- PDB-7yod: Crystal structure of A68P single mutant of O-acetylserine sulfhyd... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 7yod
Title
Crystal structure of A68P single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 A
Journal: To Be Published Title: Crystal structure of A68P single mutant of O-acetylserine sulfhydrylase from Haemophilus influenzae in complex with high-affinity inhibitory peptide from serine acetyltransferase of Salmonella typhimurium at 2.1 A Authors: Kumar, N. / Rahisuddin, R. / Saini, N. / Singh, A.K.
Resolution: 2.101→39.81 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.889 / SU B: 5.578 / SU ML: 0.153 / Cross valid method: FREE R-VALUE / ESU R: 0.279 / ESU R Free: 0.208 Details: Hydrogens have been used if present in the input file
Rfactor
Num. reflection
% reflection
Rfree
0.2553
824
4.856 %
Rwork
0.222
16143
-
all
0.224
-
-
obs
-
16967
99.959 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 37.309 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.031 Å2
-0 Å2
0 Å2
2-
-
-2.031 Å2
0 Å2
3-
-
-
4.062 Å2
Refinement step
Cycle: LAST / Resolution: 2.101→39.81 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2307
0
0
37
2344
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.012
2341
X-RAY DIFFRACTION
r_angle_refined_deg
1.519
1.633
3171
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.322
5
308
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.146
22.784
97
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.131
15
403
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.543
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.111
0.2
322
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1713
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
1134
X-RAY DIFFRACTION
r_nbtor_refined
0.305
0.2
1633
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.112
0.2
94
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.211
0.2
38
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.17
0.2
7
X-RAY DIFFRACTION
r_mcbond_it
3.001
3.578
1238
X-RAY DIFFRACTION
r_mcangle_it
4.039
5.349
1544
X-RAY DIFFRACTION
r_scbond_it
3.714
3.874
1102
X-RAY DIFFRACTION
r_scangle_it
5.174
5.648
1627
X-RAY DIFFRACTION
r_lrange_it
7.649
67.828
10190
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.101-2.155
0.335
41
0.218
1182
X-RAY DIFFRACTION
99.674
2.155-2.214
0.31
75
0.21
1141
X-RAY DIFFRACTION
100
2.214-2.278
0.315
63
0.206
1114
X-RAY DIFFRACTION
100
2.278-2.348
0.25
50
0.212
1107
X-RAY DIFFRACTION
100
2.348-2.425
0.31
44
0.227
1070
X-RAY DIFFRACTION
100
2.425-2.51
0.233
69
0.225
1011
X-RAY DIFFRACTION
100
2.51-2.605
0.25
56
0.221
961
X-RAY DIFFRACTION
100
2.605-2.711
0.296
44
0.219
961
X-RAY DIFFRACTION
100
2.711-2.832
0.255
43
0.228
923
X-RAY DIFFRACTION
100
2.832-2.97
0.231
37
0.243
897
X-RAY DIFFRACTION
100
2.97-3.13
0.269
52
0.245
808
X-RAY DIFFRACTION
100
3.13-3.32
0.187
48
0.218
800
X-RAY DIFFRACTION
100
3.32-3.548
0.32
37
0.212
732
X-RAY DIFFRACTION
100
3.548-3.832
0.2
26
0.223
707
X-RAY DIFFRACTION
100
3.832-4.197
0.219
36
0.223
645
X-RAY DIFFRACTION
100
4.197-4.691
0.276
29
0.203
576
X-RAY DIFFRACTION
100
4.691-5.413
0.258
29
0.22
511
X-RAY DIFFRACTION
100
5.413-6.622
0.304
19
0.248
452
X-RAY DIFFRACTION
100
6.622-9.333
0.215
16
0.215
349
X-RAY DIFFRACTION
100
9.333-39.81
0.234
10
0.232
198
X-RAY DIFFRACTION
98.5782
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi