- PDB-2q22: Crystal structure of uncharacterized protein (YP_323524.1) from A... -
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Basic information
Entry
Database: PDB / ID: 2q22
Title
Crystal structure of uncharacterized protein (YP_323524.1) from Anabaena variabilis ATCC 29413 at 2.11 A resolution
Components
Uncharacterized protein
Keywords
STRUCTURAL GENOMICS / UNKNOWN FUNCTION / YP_323524.1 / uncharacterized protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Protein of unknown function DUF1824 / Domain of unknown function (DUF1824) / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Uncharacterized protein
Function and homology information
Biological species
Anabaena variabilis ATCC 29413 (bacteria)
Method
X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK ... THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 2.11→29.841 Å / Num. obs: 28912 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.62 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 5.2
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
2.11-2.16
3.8
0.651
1.2
7880
2080
0.651
100
2.16-2.22
3.8
0.563
1.3
7978
2126
0.563
100
2.22-2.29
3.8
0.513
1.4
7531
1994
0.513
100
2.29-2.36
3.8
0.434
1.7
7561
2008
0.434
100
2.36-2.44
3.8
0.372
2
7257
1911
0.372
100
2.44-2.52
3.8
0.324
2.3
6955
1837
0.324
100
2.52-2.62
3.8
0.284
2.6
6800
1788
0.284
100
2.62-2.72
3.8
0.239
3.1
6487
1722
0.239
100
2.72-2.85
3.8
0.188
3.8
6242
1644
0.188
100
2.85-2.98
3.8
0.156
4.6
5928
1560
0.156
100
2.98-3.15
3.8
0.125
5.5
5712
1512
0.125
100
3.15-3.34
3.8
0.108
6.3
5339
1412
0.108
100
3.34-3.57
3.8
0.088
7.3
4995
1327
0.088
100
3.57-3.85
3.8
0.076
7.3
4754
1258
0.076
100
3.85-4.22
3.8
0.064
9.8
4259
1124
0.064
100
4.22-4.72
3.8
0.059
10.6
3964
1042
0.059
100
4.72-5.45
3.8
0.057
10.4
3424
896
0.057
100
5.45-6.67
3.8
0.064
9.9
2916
764
0.064
100
6.67-9.44
3.8
0.05
11.9
2267
593
0.05
99.9
9.44-29.84
3.7
0.051
11.4
1158
314
0.051
96.4
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
Refinement
Method to determine structure: MAD / Resolution: 2.11→29.841 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.689 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.163 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. PG4, ACT, CL AND EDO ARE MODELED BASED ON CRYSTALLIZATION/CRYO CONDITIONS. 5. THE DATA APPEAR TWINNED. IT COULD BE DUE TO THE PRESENCE OF PSEUDO-TRANSLATION. REFINEMENT CONSIDERING TWINNING DOES NOT IMPROVE MAPS OR REFINEMENT STATISTICS. AS A RESULT, THE POSSIBLE TWINNING IS NOT CONSIDERED IN THE FINAL REFINEMENT. 6. RESIDUES A/B1-7, C1-8 AND A/B/C81 ARE DISORDERED AND NOT INCLUDED IN THE FINAL MODEL.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.222
1467
5.1 %
RANDOM
Rwork
0.191
-
-
-
obs
0.193
28891
100 %
-
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: 33.42 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.75 Å2
-0.37 Å2
0 Å2
2-
-
-0.75 Å2
0 Å2
3-
-
-
1.12 Å2
Refinement step
Cycle: LAST / Resolution: 2.11→29.841 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2966
0
53
191
3210
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3084
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
2045
X-RAY DIFFRACTION
r_angle_refined_deg
1.521
2.008
4171
X-RAY DIFFRACTION
r_angle_other_deg
0.933
3
5049
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.466
5
391
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.526
24.685
111
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.518
15
517
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.002
15
7
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
483
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3363
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
560
X-RAY DIFFRACTION
r_nbd_refined
0.211
0.2
629
X-RAY DIFFRACTION
r_nbd_other
0.188
0.2
1999
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
1422
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
1691
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.168
0.2
141
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.156
0.2
15
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.209
0.2
55
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.242
0.2
20
X-RAY DIFFRACTION
r_mcbond_it
2.18
3
2100
X-RAY DIFFRACTION
r_mcbond_other
0.364
3
795
X-RAY DIFFRACTION
r_mcangle_it
3.24
5
3127
X-RAY DIFFRACTION
r_scbond_it
5.363
8
1244
X-RAY DIFFRACTION
r_scangle_it
6.998
11
1041
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
752
TIGHTPOSITIONAL
0.04
0.05
2
B
752
TIGHTPOSITIONAL
0.05
0.05
3
C
752
TIGHTPOSITIONAL
0.04
0.05
1
A
864
MEDIUMPOSITIONAL
0.17
0.5
2
B
864
MEDIUMPOSITIONAL
0.21
0.5
3
C
864
MEDIUMPOSITIONAL
0.22
0.5
1
A
752
TIGHTTHERMAL
0.19
0.5
2
B
752
TIGHTTHERMAL
0.18
0.5
3
C
752
TIGHTTHERMAL
0.19
0.5
1
A
864
MEDIUMTHERMAL
0.9
2
2
B
864
MEDIUMTHERMAL
0.95
2
3
C
864
MEDIUMTHERMAL
0.95
2
LS refinement shell
Resolution: 2.11→2.165 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.253
110
-
Rwork
0.223
1958
-
obs
-
2068
100 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.6003
-0.1997
-0.1111
2.4504
0.2238
0.5701
-0.0058
-0.0577
-0.2751
0.0336
0.0108
-0.102
0.0588
-0.0496
-0.005
-0.0579
-0.0101
0.0011
-0.0815
0.0027
-0.0741
-2.4191
41.651
5.6962
2
2.8745
1.2626
0.614
1.576
0.0557
0.9816
0.0915
0.0411
0.0413
-0.0373
-0.0767
-0.1895
-0.147
0.093
-0.0148
-0.0148
-0.0288
0.0234
-0.0226
-0.002
-0.0208
-36.9494
40.9746
7.3491
3
1.9767
0.5543
0.0354
2.9438
-0.102
1.4429
0.0434
-0.027
0.0711
0.0595
-0.0757
-0.5319
0.0488
0.2077
0.0323
-0.0244
0.027
0.0012
0.0177
0.0115
0.0345
14.2398
11.175
7.2833
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
8 - 138
9 - 139
2
X-RAY DIFFRACTION
2
B
B
8 - 138
9 - 139
3
X-RAY DIFFRACTION
3
C
C
9 - 138
10 - 139
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