0.016409
0.000000
0.000000
0.000000
0.016409
0.000000
0.000000
0.000000
0.007643
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
Partnership for Stem Cell Biology
Partnership for Stem Cell Biology (STEMCELL)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.000
90.000
90.000
60.942
60.942
130.839
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C8 H18 N2 O2
174.241
n
N-DIMETHYL-LYSINE
L-peptide linking
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
L-peptide linking
Na 1
22.990
SODIUM ION
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Plos One
1932-6203
7
e43761
e43761
10.1371/journal.pone.0043761
22984442
Structure of a Novel Winged-Helix Like Domain from Human NFRKB Protein.
2012
10.2210/pdb3u21/pdb
pdb_00003u21
100
1
double crystal monochromator
CCD
2011-06-22
MARMOSAIC 325 mm CCD
double crystal
MAD
M
x-ray
1
0.91837
1.0
0.97936
1.0
0.97915
1.0
BL9-2
SSRL
0.91837,0.97936,0.97915
SYNCHROTRON
SSRL BEAMLINE BL9-2
14504.097
Nuclear factor related to kappa-B-binding protein
2
man
polymer
22.990
SODIUM ION
1
syn
non-polymer
18.015
water
25
nat
water
DNA-binding protein R kappa-B, INO80 complex subunit G
no
yes
GLGINEISSSFFSLLLEILLLESQASLP(MSE)LEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSS
FSPFVEF(MLY)E(MLY)TQQW(MLY)LLGQSQDNE(MLY)ELAALFQLWLET(MLY)DQAFC(MLY)QENEDSS
GLGINEISSSFFSLLLEILLLESQASLPMLEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSSFSPF
VEFKEKTQQWKLLGQSQDNEKELAALFQLWLETKDQAFCKQENEDSS
A,B
421522
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
BC063280, INO80G, NFRKB
9606
Homo sapiens
562
Escherichia Coli
HK100
Plasmid
SpeedET
1
2.09
41.26
VAPOR DIFFUSION, SITTING DROP
7.5
0.09M HEPES pH 7.5, 10% glycerol, 1.26M tri-sodium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
Joint Center for Structural Genomics
JCSG
PSI:Biology
Partnership for Stem Cell Biology
STEMCELL
PSI:Biology
software
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Refinement description
Database references
Derived calculations
1
0
2011-11-02
1
1
2012-10-10
1
2
2017-11-08
1
3
2023-02-01
_software.classification
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_asym_id
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_asym_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Y
RCSB
Y
RCSB
2011-09-30
REL
REL
NA
SODIUM ION
HOH
water
1. THIS CONSTRUCT (RESIDUES 370-495) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. RESIDUE NUMBERING IS BASED ON ISOFORM 1 OF UNIPROTKB ID Q6P4R8. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.
NA
500
2
NA
NA
500
A
HOH
501
3
HOH
HOH
501
A
HOH
502
3
HOH
HOH
502
A
HOH
503
3
HOH
HOH
503
A
HOH
504
3
HOH
HOH
504
A
HOH
505
3
HOH
HOH
505
A
HOH
506
3
HOH
HOH
506
A
HOH
507
3
HOH
HOH
507
A
HOH
508
3
HOH
HOH
508
A
HOH
509
3
HOH
HOH
509
A
HOH
511
3
HOH
HOH
511
A
HOH
523
3
HOH
HOH
523
A
HOH
524
3
HOH
HOH
524
A
HOH
525
3
HOH
HOH
525
A
HOH
510
3
HOH
HOH
510
B
HOH
512
3
HOH
HOH
512
B
HOH
513
3
HOH
HOH
513
B
HOH
514
3
HOH
HOH
514
B
HOH
515
3
HOH
HOH
515
B
HOH
516
3
HOH
HOH
516
B
HOH
517
3
HOH
HOH
517
B
HOH
518
3
HOH
HOH
518
B
HOH
519
3
HOH
HOH
519
B
HOH
520
3
HOH
HOH
520
B
HOH
521
3
HOH
HOH
521
B
HOH
522
3
HOH
HOH
522
B
n
1
0
A
n
2
370
A
n
3
371
A
ILE
372
n
4
ILE
372
A
ASN
373
n
5
ASN
373
A
GLU
374
n
6
GLU
374
A
ILE
375
n
7
ILE
375
A
SER
376
n
8
SER
376
A
SER
377
n
9
SER
377
A
SER
378
n
10
SER
378
A
PHE
379
n
11
PHE
379
A
PHE
380
n
12
PHE
380
A
SER
381
n
13
SER
381
A
LEU
382
n
14
LEU
382
A
LEU
383
n
15
LEU
383
A
LEU
384
n
16
LEU
384
A
GLU
385
n
17
GLU
385
A
ILE
386
n
18
ILE
386
A
LEU
387
n
19
LEU
387
A
LEU
388
n
20
LEU
388
A
LEU
389
n
21
LEU
389
A
GLU
390
n
22
GLU
390
A
SER
391
n
23
SER
391
A
GLN
392
n
24
GLN
392
A
ALA
393
n
25
ALA
393
A
SER
394
n
26
SER
394
A
LEU
395
n
27
LEU
395
A
PRO
396
n
28
PRO
396
A
MSE
397
n
29
MSE
397
A
LEU
398
n
30
LEU
398
A
GLU
399
n
31
GLU
399
A
GLU
400
n
32
GLU
400
A
ARG
401
n
33
ARG
401
A
VAL
402
n
34
VAL
402
A
LEU
403
n
35
LEU
403
A
ASP
404
n
36
ASP
404
A
TRP
405
n
37
TRP
405
A
GLN
406
n
38
GLN
406
A
SER
407
n
39
SER
407
A
SER
408
n
40
SER
408
A
PRO
409
n
41
PRO
409
A
ALA
410
n
42
ALA
410
A
SER
411
n
43
SER
411
A
SER
412
n
44
SER
412
A
LEU
413
n
45
LEU
413
A
ASN
414
n
46
ASN
414
A
SER
415
n
47
SER
415
A
TRP
416
n
48
TRP
416
A
PHE
417
n
49
PHE
417
A
SER
418
n
50
SER
418
A
ALA
419
n
51
ALA
419
A
ALA
420
n
52
ALA
420
A
PRO
421
n
53
PRO
421
A
ASN
422
n
54
ASN
422
A
TRP
423
n
55
TRP
423
A
ALA
424
n
56
ALA
424
A
GLU
425
n
57
GLU
425
A
LEU
426
n
58
LEU
426
A
VAL
427
n
59
VAL
427
A
LEU
428
n
60
LEU
428
A
PRO
429
n
61
PRO
429
A
ALA
430
n
62
ALA
430
A
LEU
431
n
63
LEU
431
A
GLN
432
n
64
GLN
432
A
TYR
433
n
65
TYR
433
A
LEU
434
n
66
LEU
434
A
ALA
435
n
67
ALA
435
A
GLY
436
n
68
GLY
436
A
GLU
437
n
69
GLU
437
A
SER
438
n
70
SER
438
A
ARG
439
n
71
ARG
439
A
ALA
440
n
72
ALA
440
A
VAL
441
n
73
VAL
441
A
PRO
442
n
74
PRO
442
A
SER
443
n
75
SER
443
A
SER
444
n
76
SER
444
A
PHE
445
n
77
PHE
445
A
SER
446
n
78
SER
446
A
PRO
447
n
79
PRO
447
A
PHE
448
n
80
PHE
448
A
VAL
449
n
81
VAL
449
A
GLU
450
n
82
GLU
450
A
PHE
451
n
83
PHE
451
A
MLY
452
n
84
MLY
452
A
GLU
453
n
85
GLU
453
A
MLY
454
n
86
MLY
454
A
THR
455
n
87
THR
455
A
GLN
456
n
88
GLN
456
A
GLN
457
n
89
GLN
457
A
TRP
458
n
90
TRP
458
A
MLY
459
n
91
MLY
459
A
LEU
460
n
92
LEU
460
A
LEU
461
n
93
LEU
461
A
GLY
462
n
94
GLY
462
A
n
95
463
A
n
96
464
A
n
97
465
A
ASP
466
n
98
ASP
466
A
ASN
467
n
99
ASN
467
A
GLU
468
n
100
GLU
468
A
MLY
469
n
101
MLY
469
A
GLU
470
n
102
GLU
470
A
LEU
471
n
103
LEU
471
A
ALA
472
n
104
ALA
472
A
ALA
473
n
105
ALA
473
A
LEU
474
n
106
LEU
474
A
PHE
475
n
107
PHE
475
A
GLN
476
n
108
GLN
476
A
LEU
477
n
109
LEU
477
A
TRP
478
n
110
TRP
478
A
LEU
479
n
111
LEU
479
A
GLU
480
n
112
GLU
480
A
THR
481
n
113
THR
481
A
MLY
482
n
114
MLY
482
A
ASP
483
n
115
ASP
483
A
n
116
484
A
n
117
485
A
n
118
486
A
n
119
487
A
n
120
488
A
n
121
489
A
n
122
490
A
n
123
491
A
n
124
492
A
n
125
493
A
n
126
494
A
n
127
495
A
n
1
0
B
LEU
370
n
2
LEU
370
B
GLY
371
n
3
GLY
371
B
ILE
372
n
4
ILE
372
B
ASN
373
n
5
ASN
373
B
GLU
374
n
6
GLU
374
B
ILE
375
n
7
ILE
375
B
SER
376
n
8
SER
376
B
SER
377
n
9
SER
377
B
SER
378
n
10
SER
378
B
PHE
379
n
11
PHE
379
B
PHE
380
n
12
PHE
380
B
SER
381
n
13
SER
381
B
LEU
382
n
14
LEU
382
B
LEU
383
n
15
LEU
383
B
LEU
384
n
16
LEU
384
B
GLU
385
n
17
GLU
385
B
ILE
386
n
18
ILE
386
B
LEU
387
n
19
LEU
387
B
LEU
388
n
20
LEU
388
B
LEU
389
n
21
LEU
389
B
GLU
390
n
22
GLU
390
B
SER
391
n
23
SER
391
B
GLN
392
n
24
GLN
392
B
ALA
393
n
25
ALA
393
B
SER
394
n
26
SER
394
B
LEU
395
n
27
LEU
395
B
PRO
396
n
28
PRO
396
B
MSE
397
n
29
MSE
397
B
LEU
398
n
30
LEU
398
B
GLU
399
n
31
GLU
399
B
GLU
400
n
32
GLU
400
B
ARG
401
n
33
ARG
401
B
VAL
402
n
34
VAL
402
B
LEU
403
n
35
LEU
403
B
ASP
404
n
36
ASP
404
B
TRP
405
n
37
TRP
405
B
GLN
406
n
38
GLN
406
B
SER
407
n
39
SER
407
B
SER
408
n
40
SER
408
B
PRO
409
n
41
PRO
409
B
ALA
410
n
42
ALA
410
B
SER
411
n
43
SER
411
B
SER
412
n
44
SER
412
B
LEU
413
n
45
LEU
413
B
ASN
414
n
46
ASN
414
B
SER
415
n
47
SER
415
B
TRP
416
n
48
TRP
416
B
PHE
417
n
49
PHE
417
B
SER
418
n
50
SER
418
B
ALA
419
n
51
ALA
419
B
ALA
420
n
52
ALA
420
B
PRO
421
n
53
PRO
421
B
ASN
422
n
54
ASN
422
B
TRP
423
n
55
TRP
423
B
ALA
424
n
56
ALA
424
B
GLU
425
n
57
GLU
425
B
LEU
426
n
58
LEU
426
B
VAL
427
n
59
VAL
427
B
LEU
428
n
60
LEU
428
B
PRO
429
n
61
PRO
429
B
ALA
430
n
62
ALA
430
B
LEU
431
n
63
LEU
431
B
GLN
432
n
64
GLN
432
B
TYR
433
n
65
TYR
433
B
LEU
434
n
66
LEU
434
B
ALA
435
n
67
ALA
435
B
GLY
436
n
68
GLY
436
B
GLU
437
n
69
GLU
437
B
SER
438
n
70
SER
438
B
ARG
439
n
71
ARG
439
B
n
72
440
B
n
73
441
B
n
74
442
B
n
75
443
B
SER
444
n
76
SER
444
B
PHE
445
n
77
PHE
445
B
SER
446
n
78
SER
446
B
PRO
447
n
79
PRO
447
B
PHE
448
n
80
PHE
448
B
VAL
449
n
81
VAL
449
B
GLU
450
n
82
GLU
450
B
PHE
451
n
83
PHE
451
B
MLY
452
n
84
MLY
452
B
GLU
453
n
85
GLU
453
B
MLY
454
n
86
MLY
454
B
THR
455
n
87
THR
455
B
GLN
456
n
88
GLN
456
B
GLN
457
n
89
GLN
457
B
TRP
458
n
90
TRP
458
B
MLY
459
n
91
MLY
459
B
LEU
460
n
92
LEU
460
B
LEU
461
n
93
LEU
461
B
n
94
462
B
n
95
463
B
SER
464
n
96
SER
464
B
GLN
465
n
97
GLN
465
B
ASP
466
n
98
ASP
466
B
ASN
467
n
99
ASN
467
B
GLU
468
n
100
GLU
468
B
MLY
469
n
101
MLY
469
B
GLU
470
n
102
GLU
470
B
LEU
471
n
103
LEU
471
B
ALA
472
n
104
ALA
472
B
ALA
473
n
105
ALA
473
B
LEU
474
n
106
LEU
474
B
PHE
475
n
107
PHE
475
B
GLN
476
n
108
GLN
476
B
LEU
477
n
109
LEU
477
B
TRP
478
n
110
TRP
478
B
LEU
479
n
111
LEU
479
B
GLU
480
n
112
GLU
480
B
THR
481
n
113
THR
481
B
MLY
482
n
114
MLY
482
B
ASP
483
n
115
ASP
483
B
n
116
484
B
n
117
485
B
n
118
486
B
n
119
487
B
n
120
488
B
n
121
489
B
n
122
490
B
n
123
491
B
n
124
492
B
n
125
493
B
n
126
494
B
n
127
495
B
1.0635
0.6754
-0.2069
5.4284
0.1736
4.0382
-0.0925
0.0321
0.1089
-0.0577
0.1532
-0.2375
-0.3529
0.0032
-0.0607
0.1040
-0.0072
-0.0181
0.0908
-0.0191
0.0800
refined
61.0380
45.3410
53.3450
X-RAY DIFFRACTION
3.0864
0.5889
-0.5343
2.0962
-0.3884
4.4276
0.0515
-0.2075
-0.0591
0.0171
0.1051
0.1458
0.0318
-0.5040
-0.1566
0.0991
0.0091
-0.0305
0.1636
0.0487
0.0509
refined
48.6910
30.9920
75.4320
X-RAY DIFFRACTION
A
372
A
462
X-RAY DIFFRACTION
1
A
466
A
483
X-RAY DIFFRACTION
1
B
370
B
461
X-RAY DIFFRACTION
2
B
464
B
483
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
2
dimeric
1510
-23
11610
A
ASN
373
A
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
A
ILE
375
A
O
ILE
7
1_555
91.6
A
ASN
373
A
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
B
ASN
373
B
OD1
ASN
5
1_555
171.4
A
ILE
375
A
O
ILE
7
1_555
A
NA
500
C
NA
NA
1_555
B
ASN
373
B
OD1
ASN
5
1_555
88.2
A
ASN
373
A
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
B
ILE
375
B
O
ILE
7
1_555
94.2
A
ILE
375
A
O
ILE
7
1_555
A
NA
500
C
NA
NA
1_555
B
ILE
375
B
O
ILE
7
1_555
102.9
B
ASN
373
B
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
B
ILE
375
B
O
ILE
7
1_555
94.3
A
ASN
373
A
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
B
HOH
521
E
O
HOH
1_555
94.7
A
ILE
375
A
O
ILE
7
1_555
A
NA
500
C
NA
NA
1_555
B
HOH
521
E
O
HOH
1_555
164.8
B
ASN
373
B
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
B
HOH
521
E
O
HOH
1_555
83.5
B
ILE
375
B
O
ILE
7
1_555
A
NA
500
C
NA
NA
1_555
B
HOH
521
E
O
HOH
1_555
90.5
A
MSE
397
SELENOMETHIONINE
A
MSE
29
MET
A
MLY
452
N-DIMETHYL-LYSINE
A
MLY
84
LYS
A
MLY
454
N-DIMETHYL-LYSINE
A
MLY
86
LYS
A
MLY
459
N-DIMETHYL-LYSINE
A
MLY
91
LYS
A
MLY
469
N-DIMETHYL-LYSINE
A
MLY
101
LYS
A
MLY
482
N-DIMETHYL-LYSINE
A
MLY
114
LYS
B
MSE
397
SELENOMETHIONINE
B
MSE
29
MET
B
MLY
452
N-DIMETHYL-LYSINE
B
MLY
84
LYS
B
MLY
454
N-DIMETHYL-LYSINE
B
MLY
86
LYS
B
MLY
459
N-DIMETHYL-LYSINE
B
MLY
91
LYS
B
MLY
469
N-DIMETHYL-LYSINE
B
MLY
101
LYS
B
MLY
482
N-DIMETHYL-LYSINE
B
MLY
114
LYS
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ALA
393
A
N
ALA
25
A
O
TRP
458
A
O
TRP
90
A
O
MLY
459
A
O
MLY
91
A
N
GLU
450
A
N
GLU
82
B
N
ALA
393
B
N
ALA
25
B
O
TRP
458
B
O
TRP
90
B
O
MLY
459
B
O
MLY
91
B
N
GLU
450
B
N
GLU
82
1
A
CG
ARG
439
A
CG
ARG
71
1
Y
1
A
CD
ARG
439
A
CD
ARG
71
1
Y
1
A
NE
ARG
439
A
NE
ARG
71
1
Y
1
A
CZ
ARG
439
A
CZ
ARG
71
1
Y
1
A
NH1
ARG
439
A
NH1
ARG
71
1
Y
1
A
NH2
ARG
439
A
NH2
ARG
71
1
Y
1
A
CG
MLY
454
A
CG
MLY
86
1
Y
1
A
CD
MLY
454
A
CD
MLY
86
1
Y
1
A
CE
MLY
454
A
CE
MLY
86
1
Y
1
A
NZ
MLY
454
A
NZ
MLY
86
1
Y
1
A
CH1
MLY
454
A
CH1
MLY
86
1
Y
1
A
CH2
MLY
454
A
CH2
MLY
86
1
Y
1
B
CG1
ILE
372
B
CG1
ILE
4
1
Y
1
B
CG2
ILE
372
B
CG2
ILE
4
1
Y
1
B
CD1
ILE
372
B
CD1
ILE
4
1
Y
1
B
CG
ARG
439
B
CG
ARG
71
1
Y
1
B
CD
ARG
439
B
CD
ARG
71
1
Y
1
B
NE
ARG
439
B
NE
ARG
71
1
Y
1
B
CZ
ARG
439
B
CZ
ARG
71
1
Y
1
B
NH1
ARG
439
B
NH1
ARG
71
1
Y
1
B
NH2
ARG
439
B
NH2
ARG
71
1
Y
1
B
CG
MLY
454
B
CG
MLY
86
1
Y
1
B
CD
MLY
454
B
CD
MLY
86
1
Y
1
B
CE
MLY
454
B
CE
MLY
86
1
Y
1
B
NZ
MLY
454
B
NZ
MLY
86
1
Y
1
B
CH1
MLY
454
B
CH1
MLY
86
1
Y
1
B
CH2
MLY
454
B
CH2
MLY
86
1
Y
1
B
CG
GLN
465
B
CG
GLN
97
1
Y
1
B
CD
GLN
465
B
CD
GLN
97
1
Y
1
B
OE1
GLN
465
B
OE1
GLN
97
1
Y
1
B
NE2
GLN
465
B
NE2
GLN
97
1
Y
1
B
CG
ASP
483
B
CG
ASP
115
1
Y
1
B
OD1
ASP
483
B
OD1
ASP
115
1
Y
1
B
OD2
ASP
483
B
OD2
ASP
115
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
LEU
370
A
LEU
2
1
Y
1
A
GLY
371
A
GLY
3
1
Y
1
A
GLN
463
A
GLN
95
1
Y
1
A
SER
464
A
SER
96
1
Y
1
A
GLN
465
A
GLN
97
1
Y
1
A
GLN
484
A
GLN
116
1
Y
1
A
ALA
485
A
ALA
117
1
Y
1
A
PHE
486
A
PHE
118
1
Y
1
A
CYS
487
A
CYS
119
1
Y
1
A
MLY
488
A
MLY
120
1
Y
1
A
GLN
489
A
GLN
121
1
Y
1
A
GLU
490
A
GLU
122
1
Y
1
A
ASN
491
A
ASN
123
1
Y
1
A
GLU
492
A
GLU
124
1
Y
1
A
ASP
493
A
ASP
125
1
Y
1
A
SER
494
A
SER
126
1
Y
1
A
SER
495
A
SER
127
1
Y
1
B
GLY
0
B
GLY
1
1
Y
1
B
ALA
440
B
ALA
72
1
Y
1
B
VAL
441
B
VAL
73
1
Y
1
B
PRO
442
B
PRO
74
1
Y
1
B
SER
443
B
SER
75
1
Y
1
B
GLY
462
B
GLY
94
1
Y
1
B
GLN
463
B
GLN
95
1
Y
1
B
GLN
484
B
GLN
116
1
Y
1
B
ALA
485
B
ALA
117
1
Y
1
B
PHE
486
B
PHE
118
1
Y
1
B
CYS
487
B
CYS
119
1
Y
1
B
MLY
488
B
MLY
120
1
Y
1
B
GLN
489
B
GLN
121
1
Y
1
B
GLU
490
B
GLU
122
1
Y
1
B
ASN
491
B
ASN
123
1
Y
1
B
GLU
492
B
GLU
124
1
Y
1
B
ASP
493
B
ASP
125
1
Y
1
B
SER
494
B
SER
126
1
Y
1
B
SER
495
B
SER
127
1
Y
1
A
GLU
390
75.84
-47.01
1
A
SER
391
70.91
-47.25
1
A
SER
444
-98.95
45.58
1
B
SER
391
74.11
-58.79
1
B
ASP
466
64.73
-1.97
97.070
46.2329
25.430
-0.2100
0.0000
0.0000
-0.2100
0.0000
0.4300
0.9290
0.9050
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. SODIUM ION (NA) FROM CRYSTALLIZATION CONDITION WAS MODELED.
0.2695
0.2305
0.2324
2.1800
35.466
662
13504
4.9000
99.7500
1.000
0.370
12.5180
0.1560
RANDOM
1
THROUGHOUT
0.000
MAD
0.2220
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.1800
35.466
25
1758
1
0
1732
0.012
0.022
1780
0.001
0.020
1163
1.252
1.978
2425
0.866
3.000
2861
5.482
5.000
214
37.308
26.104
77
15.037
15.133
301
7.053
15.000
2
0.070
0.200
279
0.006
0.021
1922
0.001
0.020
338
2.782
3.895
1780
0.478
3.917
1163
4.176
8.643
2424
2.448
8.825
2861
6.824
17.777
594
1
A
1
1360
X-RAY DIFFRACTION
MEDIUM POSITIONAL
0.230
0.500
1
A
1
1360
X-RAY DIFFRACTION
MEDIUM THERMAL
2.310
2.000
0.2890
0.2520
2.2360
40
809
849
20
99.8800
41.259
2.18
35.466
3U21
13560
-3.000
0.067
1
20.780
99.800
0.796
2.180
2.260
2.4
9710
1360
1
99.900
0.624
2.260
2.350
3.1
9264
1298
1
99.800
0.506
2.350
2.450
3.8
8939
1247
1
100.000
0.365
2.450
2.580
5.3
9488
1332
1
100.000
0.248
2.580
2.750
7.9
10006
1409
1
100.000
0.152
2.750
2.960
12.2
9368
1322
1
100.000
0.101
2.960
3.250
18.1
9300
1316
1
100.000
0.047
3.250
3.720
35.2
9515
1369
1
99.900
0.029
3.720
4.680
53.2
9606
1407
1
99.900
0.024
4.680
58.9
9421
1500
1
98.300
model building
D.C. & J.S. Richardson lab
molprobity@kinemage.biochem.duke.edu
http://kinemage.biochem.duke.edu/molprobity/
MolProbity
package
3beta29
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
phasing
Eric de La Fortelle
sharp-develop@globalphasing.com
http://www.globalphasing.com/sharp/
SHARP
package
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
December 6, 2010
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.6.0116
data reduction
XDS
phasing
SHELXD
Crystal structure of a Fragment of Nuclear factor related to kappa-B-binding protein (residues 370-495) (NFRKB) from Homo sapiens at 2.18 A resolution
1
N
N
1
N
N
2
N
N
3
N
N
3
N
N
CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
A
SER
378
A
SER
10
HELX_P
A
LEU
389
A
LEU
21
1
1
12
A
LEU
395
A
LEU
27
HELX_P
A
SER
407
A
SER
39
1
2
13
A
SER
408
A
SER
40
HELX_P
A
ASN
414
A
ASN
46
5
3
7
A
TRP
416
A
TRP
48
HELX_P
A
ALA
420
A
ALA
52
5
4
5
A
TRP
423
A
TRP
55
HELX_P
A
GLU
425
A
GLU
57
5
5
3
A
LEU
426
A
LEU
58
HELX_P
A
ALA
435
A
ALA
67
1
6
10
A
ASN
467
A
ASN
99
HELX_P
A
MLY
482
A
MLY
114
1
7
16
B
SER
378
B
SER
10
HELX_P
B
SER
391
B
SER
23
1
8
14
B
SER
394
B
SER
26
HELX_P
B
SER
408
B
SER
40
1
9
15
B
PRO
409
B
PRO
41
HELX_P
B
ASN
414
B
ASN
46
5
10
6
B
TRP
416
B
TRP
48
HELX_P
B
ALA
420
B
ALA
52
5
11
5
B
ASN
422
B
ASN
54
HELX_P
B
GLU
425
B
GLU
57
5
12
4
B
LEU
426
B
LEU
58
HELX_P
B
ALA
435
B
ALA
67
1
13
10
B
ASN
467
B
ASN
99
HELX_P
B
MLY
482
B
MLY
114
1
14
16
covale
1.335
both
A
PRO
396
A
C
PRO
28
1_555
A
MSE
397
A
N
MSE
29
1_555
covale
1.329
both
A
MSE
397
A
C
MSE
29
1_555
A
LEU
398
A
N
LEU
30
1_555
covale
1.328
both
A
PHE
451
A
C
PHE
83
1_555
A
MLY
452
A
N
MLY
84
1_555
covale
1.330
both
A
MLY
452
A
C
MLY
84
1_555
A
GLU
453
A
N
GLU
85
1_555
covale
1.333
both
A
GLU
453
A
C
GLU
85
1_555
A
MLY
454
A
N
MLY
86
1_555
covale
1.339
both
A
MLY
454
A
C
MLY
86
1_555
A
THR
455
A
N
THR
87
1_555
covale
1.333
both
A
TRP
458
A
C
TRP
90
1_555
A
MLY
459
A
N
MLY
91
1_555
covale
1.327
both
A
MLY
459
A
C
MLY
91
1_555
A
LEU
460
A
N
LEU
92
1_555
covale
1.328
both
A
GLU
468
A
C
GLU
100
1_555
A
MLY
469
A
N
MLY
101
1_555
covale
1.329
both
A
MLY
469
A
C
MLY
101
1_555
A
GLU
470
A
N
GLU
102
1_555
covale
1.333
both
A
THR
481
A
C
THR
113
1_555
A
MLY
482
A
N
MLY
114
1_555
covale
1.327
both
A
MLY
482
A
C
MLY
114
1_555
A
ASP
483
A
N
ASP
115
1_555
covale
1.331
both
B
PRO
396
B
C
PRO
28
1_555
B
MSE
397
B
N
MSE
29
1_555
covale
1.335
both
B
MSE
397
B
C
MSE
29
1_555
B
LEU
398
B
N
LEU
30
1_555
covale
1.327
both
B
PHE
451
B
C
PHE
83
1_555
B
MLY
452
B
N
MLY
84
1_555
covale
1.321
both
B
MLY
452
B
C
MLY
84
1_555
B
GLU
453
B
N
GLU
85
1_555
covale
1.334
both
B
GLU
453
B
C
GLU
85
1_555
B
MLY
454
B
N
MLY
86
1_555
covale
1.332
both
B
MLY
454
B
C
MLY
86
1_555
B
THR
455
B
N
THR
87
1_555
covale
1.337
both
B
TRP
458
B
C
TRP
90
1_555
B
MLY
459
B
N
MLY
91
1_555
covale
1.325
both
B
MLY
459
B
C
MLY
91
1_555
B
LEU
460
B
N
LEU
92
1_555
covale
1.323
both
B
GLU
468
B
C
GLU
100
1_555
B
MLY
469
B
N
MLY
101
1_555
covale
1.320
both
B
MLY
469
B
C
MLY
101
1_555
B
GLU
470
B
N
GLU
102
1_555
covale
1.332
both
B
THR
481
B
C
THR
113
1_555
B
MLY
482
B
N
MLY
114
1_555
covale
1.331
both
B
MLY
482
B
C
MLY
114
1_555
B
ASP
483
B
N
ASP
115
1_555
metalc
2.395
A
ASN
373
A
OD1
ASN
5
1_555
A
NA
500
C
NA
NA
1_555
metalc
2.373
A
ILE
375
A
O
ILE
7
1_555
A
NA
500
C
NA
NA
1_555
metalc
2.285
A
NA
500
C
NA
NA
1_555
B
ASN
373
B
OD1
ASN
5
1_555
metalc
2.334
A
NA
500
C
NA
NA
1_555
B
ILE
375
B
O
ILE
7
1_555
metalc
2.273
A
NA
500
C
NA
NA
1_555
B
HOH
521
E
O
HOH
1_555
Transcription regulation, DNA BINDING
DNA/RNA-binding 3-helical bundle, winged-HTH domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, Transcription regulation, DNA BINDING PROTEIN, DNA BINDING, Partnership for Stem Cell Biology, STEMCELL
A
B
A
372
A
437
4
B
372
B
437
4
A
445
A
483
4
B
445
B
483
4
NFRKB_HUMAN
UNP
1
370
Q6P4R8
LGINEISSSFFSLLLEILLLESQASLPMLEERVLDWQSSPASSLNSWFSAAPNWAELVLPALQYLAGESRAVPSSFSPFV
EFKEKTQQWKLLGQSQDNEKELAALFQLWLETKDQAFCKQENEDSS
370
495
3U21
370
495
Q6P4R8
A
1
2
127
370
495
3U21
370
495
Q6P4R8
B
1
2
127
1
expression tag
GLY
0
3U21
A
Q6P4R8
UNP
1
2
expression tag
GLY
0
3U21
B
Q6P4R8
UNP
1
3
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLN
392
A
GLN
24
A
SER
394
A
SER
26
A
GLN
457
A
GLN
89
A
LEU
460
A
LEU
92
A
VAL
449
A
VAL
81
A
MLY
452
A
MLY
84
B
GLN
392
B
GLN
24
B
ALA
393
B
ALA
25
B
GLN
457
B
GLN
89
B
LEU
460
B
LEU
92
B
VAL
449
B
VAL
81
B
MLY
452
B
MLY
84
BINDING SITE FOR RESIDUE NA A 500
A
NA
500
Software
5
A
ASN
373
A
ASN
5
5
1_555
A
ILE
375
A
ILE
7
5
1_555
B
ASN
373
B
ASN
5
5
1_555
B
ILE
375
B
ILE
7
5
1_555
B
HOH
521
E
HOH
5
1_555
96
P 43 21 2