0.020627
0.000000
0.006890
0.000000
0.029369
0.000000
0.000000
0.000000
0.020143
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
Partnership for Nuclear Receptor Signaling Code Biology (NHRS)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
108.470
90.000
48.480
34.050
52.340
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
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-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
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
To be published
0353
Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution
10.2210/pdb4zey/pdb
pdb_00004zey
100
1
Vertical focusing mirror; double crystal Si(111) monochromator
CCD
2014-12-05
MARMOSAIC 325 mm CCD
double crystal Si(111)
MAD
M
x-ray
1
0.95369
1.0
0.97968
1.0
0.97943
1.0
BL14-1
SSRL
0.95369,0.97968,0.97943
SYNCHROTRON
SSRL BEAMLINE BL14-1
9855.853
Nuclear receptor-binding factor 2
UNP residues 4-86
1
man
polymer
96.063
SULFATE ION
2
syn
non-polymer
18.015
water
102
nat
water
NRBF-2,Comodulator of PPAR and RXR
no
yes
G(MSE)EGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEA(MSE)KLTQSEQAHLSLELQRDSH(MSE)KQLLL
IQERWKRAQREERLKA
GMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREE
RLKA
A
JCSG-429611
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
Human
sample
1
84
NRBF2, COPR
9606
Homo sapiens
562
Escherichia Coli
PB1
Plasmid
Biological sequence
SpeedET
1
2.08
40.83
VAPOR DIFFUSION, SITTING DROP
25.0% Glycerol, 1.50M ammonium sulfate
293
Joint Center for Structural Genomics
JCSG
PSI:Biology
Partnership for Nuclear Receptor Signaling Code Biology
NHRs
PSI:Biology
audit_author
entity_src_gen
pdbx_struct_oper_list
software
citation_author
database_2
struct_ref_seq_dif
repository
Initial release
Derived calculations
Refinement description
Source and taxonomy
Structure summary
Database references
Database references
1
0
2015-05-06
1
1
2017-11-22
1
2
2018-01-24
1
3
2023-02-01
_audit_author.name
_entity_src_gen.pdbx_alt_source_flag
_pdbx_struct_oper_list.symmetry_operation
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2015-04-20
REL
REL
SO4
SULFATE ION
HOH
water
THE CONSTRUCT (4-86) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
SO4
401
2
SO4
SO4
401
A
SO4
402
2
SO4
SO4
402
A
HOH
427
3
HOH
HOH
501
A
HOH
425
3
HOH
HOH
502
A
HOH
422
3
HOH
HOH
503
A
HOH
435
3
HOH
HOH
504
A
HOH
433
3
HOH
HOH
505
A
HOH
447
3
HOH
HOH
506
A
HOH
455
3
HOH
HOH
507
A
HOH
436
3
HOH
HOH
508
A
HOH
491
3
HOH
HOH
509
A
HOH
417
3
HOH
HOH
510
A
HOH
463
3
HOH
HOH
511
A
HOH
430
3
HOH
HOH
512
A
HOH
419
3
HOH
HOH
513
A
HOH
453
3
HOH
HOH
514
A
HOH
450
3
HOH
HOH
515
A
HOH
411
3
HOH
HOH
516
A
HOH
449
3
HOH
HOH
517
A
HOH
442
3
HOH
HOH
518
A
HOH
428
3
HOH
HOH
519
A
HOH
467
3
HOH
HOH
520
A
HOH
420
3
HOH
HOH
521
A
HOH
408
3
HOH
HOH
522
A
HOH
434
3
HOH
HOH
523
A
HOH
437
3
HOH
HOH
524
A
HOH
406
3
HOH
HOH
525
A
HOH
403
3
HOH
HOH
526
A
HOH
409
3
HOH
HOH
527
A
HOH
421
3
HOH
HOH
528
A
HOH
487
3
HOH
HOH
529
A
HOH
415
3
HOH
HOH
530
A
HOH
488
3
HOH
HOH
531
A
HOH
446
3
HOH
HOH
532
A
HOH
429
3
HOH
HOH
533
A
HOH
439
3
HOH
HOH
534
A
HOH
457
3
HOH
HOH
535
A
HOH
413
3
HOH
HOH
536
A
HOH
445
3
HOH
HOH
537
A
HOH
464
3
HOH
HOH
538
A
HOH
412
3
HOH
HOH
539
A
HOH
458
3
HOH
HOH
540
A
HOH
424
3
HOH
HOH
541
A
HOH
503
3
HOH
HOH
542
A
HOH
438
3
HOH
HOH
543
A
HOH
461
3
HOH
HOH
544
A
HOH
451
3
HOH
HOH
545
A
HOH
471
3
HOH
HOH
546
A
HOH
462
3
HOH
HOH
547
A
HOH
468
3
HOH
HOH
548
A
HOH
490
3
HOH
HOH
549
A
HOH
497
3
HOH
HOH
550
A
HOH
459
3
HOH
HOH
551
A
HOH
493
3
HOH
HOH
552
A
HOH
452
3
HOH
HOH
553
A
HOH
444
3
HOH
HOH
554
A
HOH
407
3
HOH
HOH
555
A
HOH
431
3
HOH
HOH
556
A
HOH
454
3
HOH
HOH
557
A
HOH
476
3
HOH
HOH
558
A
HOH
469
3
HOH
HOH
559
A
HOH
478
3
HOH
HOH
560
A
HOH
410
3
HOH
HOH
561
A
HOH
480
3
HOH
HOH
562
A
HOH
466
3
HOH
HOH
563
A
HOH
485
3
HOH
HOH
564
A
HOH
423
3
HOH
HOH
565
A
HOH
414
3
HOH
HOH
566
A
HOH
443
3
HOH
HOH
567
A
HOH
492
3
HOH
HOH
568
A
HOH
426
3
HOH
HOH
569
A
HOH
404
3
HOH
HOH
570
A
HOH
473
3
HOH
HOH
571
A
HOH
498
3
HOH
HOH
572
A
HOH
460
3
HOH
HOH
573
A
HOH
405
3
HOH
HOH
574
A
HOH
475
3
HOH
HOH
575
A
HOH
448
3
HOH
HOH
576
A
HOH
440
3
HOH
HOH
577
A
HOH
456
3
HOH
HOH
578
A
HOH
432
3
HOH
HOH
579
A
HOH
484
3
HOH
HOH
580
A
HOH
479
3
HOH
HOH
581
A
HOH
441
3
HOH
HOH
582
A
HOH
416
3
HOH
HOH
583
A
HOH
486
3
HOH
HOH
584
A
HOH
465
3
HOH
HOH
585
A
HOH
504
3
HOH
HOH
586
A
HOH
496
3
HOH
HOH
587
A
HOH
489
3
HOH
HOH
588
A
HOH
495
3
HOH
HOH
589
A
HOH
418
3
HOH
HOH
590
A
HOH
482
3
HOH
HOH
591
A
HOH
477
3
HOH
HOH
592
A
HOH
474
3
HOH
HOH
593
A
HOH
470
3
HOH
HOH
594
A
HOH
502
3
HOH
HOH
595
A
HOH
501
3
HOH
HOH
596
A
HOH
483
3
HOH
HOH
597
A
HOH
500
3
HOH
HOH
598
A
HOH
494
3
HOH
HOH
599
A
HOH
481
3
HOH
HOH
600
A
HOH
472
3
HOH
HOH
601
A
HOH
499
3
HOH
HOH
602
A
GLY
0
n
1
GLY
0
A
MSE
4
n
2
MSE
4
A
GLU
5
n
3
GLU
5
A
GLY
6
n
4
GLY
6
A
PRO
7
n
5
PRO
7
A
LEU
8
n
6
LEU
8
A
ASN
9
n
7
ASN
9
A
LEU
10
n
8
LEU
10
A
ALA
11
n
9
ALA
11
A
HIS
12
n
10
HIS
12
A
GLN
13
n
11
GLN
13
A
GLN
14
n
12
GLN
14
A
SER
15
n
13
SER
15
A
ARG
16
n
14
ARG
16
A
ARG
17
n
15
ARG
17
A
ALA
18
n
16
ALA
18
A
ASP
19
n
17
ASP
19
A
ARG
20
n
18
ARG
20
A
LEU
21
n
19
LEU
21
A
LEU
22
n
20
LEU
22
A
ALA
23
n
21
ALA
23
A
ALA
24
n
22
ALA
24
A
GLY
25
n
23
GLY
25
A
LYS
26
n
24
LYS
26
A
TYR
27
n
25
TYR
27
A
GLU
28
n
26
GLU
28
A
GLU
29
n
27
GLU
29
A
ALA
30
n
28
ALA
30
A
ILE
31
n
29
ILE
31
A
SER
32
n
30
SER
32
A
CYS
33
n
31
CYS
33
A
HIS
34
n
32
HIS
34
A
LYS
35
n
33
LYS
35
A
LYS
36
n
34
LYS
36
A
ALA
37
n
35
ALA
37
A
ALA
38
n
36
ALA
38
A
ALA
39
n
37
ALA
39
A
TYR
40
n
38
TYR
40
A
LEU
41
n
39
LEU
41
A
SER
42
n
40
SER
42
A
GLU
43
n
41
GLU
43
A
ALA
44
n
42
ALA
44
A
MSE
45
n
43
MSE
45
A
LYS
46
n
44
LYS
46
A
LEU
47
n
45
LEU
47
A
THR
48
n
46
THR
48
A
GLN
49
n
47
GLN
49
A
SER
50
n
48
SER
50
A
GLU
51
n
49
GLU
51
A
GLN
52
n
50
GLN
52
A
ALA
53
n
51
ALA
53
A
HIS
54
n
52
HIS
54
A
LEU
55
n
53
LEU
55
A
SER
56
n
54
SER
56
A
LEU
57
n
55
LEU
57
A
GLU
58
n
56
GLU
58
A
LEU
59
n
57
LEU
59
A
GLN
60
n
58
GLN
60
A
ARG
61
n
59
ARG
61
A
ASP
62
n
60
ASP
62
A
SER
63
n
61
SER
63
A
HIS
64
n
62
HIS
64
A
MSE
65
n
63
MSE
65
A
LYS
66
n
64
LYS
66
A
GLN
67
n
65
GLN
67
A
LEU
68
n
66
LEU
68
A
LEU
69
n
67
LEU
69
A
LEU
70
n
68
LEU
70
A
ILE
71
n
69
ILE
71
A
GLN
72
n
70
GLN
72
A
GLU
73
n
71
GLU
73
A
ARG
74
n
72
ARG
74
A
TRP
75
n
73
TRP
75
A
LYS
76
n
74
LYS
76
A
ARG
77
n
75
ARG
77
A
ALA
78
n
76
ALA
78
A
GLN
79
n
77
GLN
79
A
ARG
80
n
78
ARG
80
A
GLU
81
n
79
GLU
81
A
GLU
82
n
80
GLU
82
A
ARG
83
n
81
ARG
83
A
LEU
84
n
82
LEU
84
A
LYS
85
n
83
LYS
85
A
ALA
86
n
84
ALA
86
A
0.7284
0.2111
0.4411
0.4439
0.3387
1.0412
0.0285
0.0443
0.0377
-0.0622
0.0025
-0.0372
-0.0164
0.0212
-0.0310
-0.0469
0.0081
0.0891
0.0666
0.0008
-0.0762
refined
5.8667
5.6877
-6.0783
X-RAY DIFFRACTION
A
0
A
86
X-RAY DIFFRACTION
1
{A|0 - 86}
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
2
dimeric
2680
-46
10210
A
MSE
4
modified residue
A
MSE
2
MET
A
MSE
45
modified residue
A
MSE
43
MET
A
MSE
65
modified residue
A
MSE
63
MET
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
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
2_555
-x,y,-z
crystal symmetry operation
0.0000000000
0.0000000000
0.0000000000
1
A
SO4
401
B
SO4
1
A
HOH
548
D
HOH
1
A
MSE
4
-37.68
144.07
89.890
25.7253
11.970
1.4756
0.0000
0.5040
-2.3193
0.0000
0.8436
0.9483
0.9332
1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. 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. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
0.2482
0.2089
0.2107
1.5000
27.366
618
12871
4.8000
97.9200
1.000
0.500
RANDOM
1
THROUGHOUT
0.000
MAD
0.201
1.5000
27.366
102
791
10
0
679
357
SINUSOIDAL
2.000
21
HARMONIC
2.000
100
HARMONIC
5.000
702
HARMONIC
20.000
85
SEMIHARMONIC
5.000
907
SEMIHARMONIC
4.000
0.010
702
HARMONIC
2.000
0.900
938
HARMONIC
2.000
2.490
2.490
0.1999
0.1881
0.1886
1.6400
144
2919
3063
6
4.7000
97.9200
17.415
0.984
1.50
27.366
4ZEY
12873
-3.000
0.092
0.128
1
7.560
39652
1.685
92.400
0.782
0.392
1.500
1.550
1.8
3742
2425
2234
0.538
1
92.100
0.860
0.320
1.550
1.620
2.0
4494
2851
2661
0.439
93.300
0.907
0.252
1.620
1.690
2.6
3697
2353
2188
0.346
93.000
0.920
0.215
1.690
1.780
3.2
4090
2605
2432
0.297
93.400
0.962
0.153
1.780
1.890
4.3
3888
2510
2319
0.211
92.400
0.966
0.122
1.890
2.040
5.8
3937
2586
2363
0.171
91.400
0.979
0.086
2.040
2.240
8.6
3605
2467
2193
0.121
88.900
0.958
0.102
2.240
2.560
11.4
3869
2542
2305
0.143
90.700
0.942
0.111
2.560
3.230
15.3
4294
2580
2491
0.155
96.600
0.986
0.057
3.230
20.4
4036
2555
2341
0.080
91.600
data extraction
PDB_EXTRACT
3.10
phasing
SOLVE
data scaling
XSCALE
November 3, 2014 BUILT=20141118
refinement
BUSTER-TNT
2.10.2
refinement
BUSTER
2.10.2
data reduction
XDS
Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution
1
N
N
2
N
N
2
N
N
3
N
N
A
GLY
6
A
GLY
4
HELX_P
A
ALA
24
A
ALA
22
1
AA1
19
A
LYS
26
A
LYS
24
HELX_P
A
LYS
46
A
LYS
44
1
AA2
21
A
SER
50
A
SER
48
HELX_P
A
ALA
86
A
ALA
84
1
AA3
37
covale
1.359
both
A
GLY
0
A
C
GLY
1
1_555
A
MSE
4
A
N
MSE
2
1_555
covale
1.348
both
A
MSE
4
A
C
MSE
2
1_555
A
GLU
5
A
N
GLU
3
1_555
covale
1.338
both
A
ALA
44
A
C
ALA
42
1_555
A
MSE
45
A
N
MSE
43
1_555
covale
1.341
both
A
MSE
45
A
C
MSE
43
1_555
A
LYS
46
A
N
LYS
44
1_555
covale
1.360
both
A
HIS
64
A
C
HIS
62
1_555
A
MSE
65
A
N
MSE
63
1_555
covale
1.354
both
A
MSE
65
A
C
MSE
63
1_555
A
LYS
66
A
N
LYS
64
1_555
TRANSCRIPTION REGULATOR
Structural Genomics, Joint Center for Structural Genomics, JCSG, Partnership for Nuclear Receptor Signaling Code Biology, NHRs, PSI-BIOLOGY, TRANSCRIPTION REGULATOR
NRBF2_HUMAN
UNP
1
4
Q96F24
MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREER
LKA
4
86
4ZEY
4
86
Q96F24
A
1
2
84
1
expression tag
GLY
0
4ZEY
A
Q96F24
UNP
1
binding site for residue SO4 A 401
A
SO4
401
Software
6
binding site for residue SO4 A 402
A
SO4
402
Software
6
A
HIS
12
A
HIS
10
6
2_555
A
HIS
12
A
HIS
10
6
1_555
A
SER
15
A
SER
13
6
1_555
A
SER
15
A
SER
13
6
2_555
A
HOH
548
D
HOH
6
2_555
A
HOH
548
D
HOH
6
1_555
A
TRP
75
A
TRP
73
6
1_555
A
GLN
79
A
GLN
77
6
2_554
A
GLN
79
A
GLN
77
6
1_555
A
HOH
504
D
HOH
6
1_555
A
HOH
552
D
HOH
6
1_555
A
HOH
552
D
HOH
6
2_554
5
C 1 2 1