1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Maltsev, A.
Grishaev, A.
Roche, J.
Zasloff, M.
Bax, A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
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
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 S
149.211
y
METHIONINE
L-peptide linking
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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
136
3752
3755
10.1021/ja4132642
24568736
Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.
2014
10.2210/pdb2mjb/pdb
pdb_00002mjb
8576.831
Ubiquitin-60S ribosomal protein L40
Ubiquitin-like 3 domain
1
man
polymer
CEP52, Ubiquitin A-52 residue ribosomal protein fusion product 1, Ubiquitin, 60S ribosomal protein L40, Ubiquitin-40S ribosomal protein S27a, Ubiquitin carboxyl extension protein 80, Ubiquitin, 40S ribosomal protein S27a, Polyubiquitin-B, Ubiquitin, Polyubiquitin-C, Ubiquitin
no
no
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
A
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
human
sample
UBA52, UBCEP2, RPS27A, UBA80, UBCEP1, UBB, UBC
9606
Homo sapiens
511693
Escherichia coli
BL21
PET11A
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Data collection
Database references
Other
1
0
2014-03-26
1
1
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
Solution nmr structure of ubiquitin refined against dipolar couplings in 2 media
BMRB
Y
RCSB
2014-01-02
REL
REL
REL
REL
2754
35
64
6.9
all calculated structures submitted
20
20
0.024
2D 1H-15N IPAP HSQC
2D 1H-15N IPAP HSQC
2D 1H-15N TROSY HSQC
2D 1H-15N TROSY HSQC
3D TROSY HNCO
3D TROSY HNCO
3D HN(CO)CA 1H-1H decoupled
1H-15N ARTSY
0.5
mM
[U-100% 13C; U-100% 15N; U-100% 2H]
20
mM
[U-100% 2H]
4.8
mM
1.5
mM
10
mM
0.5
mM
[U-100% 13C; U-100% 15N; U-100% 2H]
20
mM
[U-100% 2H]
1.5
mM
10
mM
0.6
mM
[U-100% 13C; U-100% 15N]
13
mg/mL
140
mM
0.8
mM
[U-100% 13C; U-100% 15N; U-100% 2H]
14
mg/mL
150
mM
6.0
ambient
308
K
6.0
ambient
298
K
Refinement against residual dipolar couplings in 4 alignment media, distance, dihedral angle, and through-H bond (N/C) J-coupling restraints with hydrogen-bonding database potential starting from the coordinates of 1D3Z entry.
simulated annealing
1
closest to the average
0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 4.8 mM squalamine, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O
95% H2O/5% D2O
0.5 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 20 mM [U-100% 2H] D4-imidazole, 1.5 mM hexanol, 10 mM sodium phosphate, 95% H2O/5% D2O
95% H2O/5% D2O
0.6 mM [U-100% 13C; U-100% 15N] ubiquitin, 13 mg/mL Pf1 phage, 140 mM sodium chloride, 95% H2O/5% D2O
95% H2O/5% D2O
0.8 mM [U-100% 13C; U-100% 15N; U-100% 2H] ubiquitin, 14 mg/mL Pf1 phage, 150 mM sodium chloride, 95% H2O/5% D2O
95% H2O/5% D2O
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
data analysis
NMRPipe
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
500
Bruker
AVANCE
Bruker Avance
600
Bruker
AVANCE
Bruker Avance
800
Bruker
AVANCE
Bruker Avance
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
GLU
16
n
16
GLU
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
PRO
19
n
19
PRO
19
A
SER
20
n
20
SER
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
ILE
23
n
23
ILE
23
A
GLU
24
n
24
GLU
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
GLN
31
n
31
GLN
31
A
ASP
32
n
32
ASP
32
A
LYS
33
n
33
LYS
33
A
GLU
34
n
34
GLU
34
A
GLY
35
n
35
GLY
35
A
ILE
36
n
36
ILE
36
A
PRO
37
n
37
PRO
37
A
PRO
38
n
38
PRO
38
A
ASP
39
n
39
ASP
39
A
GLN
40
n
40
GLN
40
A
GLN
41
n
41
GLN
41
A
ARG
42
n
42
ARG
42
A
LEU
43
n
43
LEU
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
LYS
48
n
48
LYS
48
A
GLN
49
n
49
GLN
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
GLY
53
n
53
GLY
53
A
ARG
54
n
54
ARG
54
A
THR
55
n
55
THR
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
ASP
58
n
58
ASP
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
ILE
61
n
61
ILE
61
A
GLN
62
n
62
GLN
62
A
LYS
63
n
63
LYS
63
A
GLU
64
n
64
GLU
64
A
SER
65
n
65
SER
65
A
THR
66
n
66
THR
66
A
LEU
67
n
67
LEU
67
A
HIS
68
n
68
HIS
68
A
LEU
69
n
69
LEU
69
A
VAL
70
n
70
VAL
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
LEU
73
n
73
LEU
73
A
ARG
74
n
74
ARG
74
A
GLY
75
n
75
GLY
75
A
GLY
76
n
76
GLY
76
A
author_defined_assembly
1
monomeric
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
O
ILE
13
A
O
ILE
13
A
N
VAL
5
A
N
VAL
5
A
N
PHE
4
A
N
PHE
4
A
O
LEU
67
A
O
LEU
67
A
O
HIS
68
A
O
HIS
68
A
N
ILE
44
A
N
ILE
44
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
4
A
ARG
74
-139.84
-54.44
12
A
ARG
74
-149.35
-56.89
18
A
LEU
73
-160.25
114.36
closest to the average, model1
Solution nmr structure of ubiquitin refined against dipolar couplings in 4 media
1
N
N
A
THR
22
A
THR
22
HELX_P
A
GLY
35
A
GLY
35
1
1
14
A
PRO
37
A
PRO
37
HELX_P
A
ASP
39
A
ASP
39
5
2
3
A
LEU
56
A
LEU
56
HELX_P
A
ASN
60
A
ASN
60
5
3
5
SIGNALING PROTEIN
RESIDUAL DIPOLAR COUPLING, SQUALAMINE, SIGNALING PROTEIN
RL40_HUMAN
UNP
1
153
P62987
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIF
VKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
229
304
2MJB
1
76
P62987
A
1
1
76
5
anti-parallel
parallel
anti-parallel
anti-parallel
A
THR
12
A
THR
12
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
LYS
6
A
LYS
6
A
THR
66
A
THR
66
A
LEU
71
A
LEU
71
A
GLN
41
A
GLN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49