1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Newlove, T.
Atkinson, K.R.
Van Dorn, L.O.
Cordes, M.H.
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
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
Biochemistry
BICHAW
0033
0006-2960
45
6379
6391
10.1021/bi052541c
16700549
A Trade between Similar but Nonequivalent Intrasubunit and Intersubunit Contacts in Cro Dimer Evolution.
2006
10.2210/pdb2a63/pdb
pdb_00002a63
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
7423.485
Regulatory protein cro
A33W, F58D, Y26Q
1
man
polymer
no
no
MEQRITLKDYAMRFGQTKTAKDLGVQQSAINKWIHAGRKIFLTINADGSVYAEEVKPDPSNKKTTA
MEQRITLKDYAMRFGQTKTAKDLGVQQSAINKWIHAGRKIFLTINADGSVYAEEVKPDPSNKKTTA
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
Lambda-like viruses
Escherichia
Escherichia coli
sample
cro
10710
Enterobacteria phage lambda
469008
Escherichia coli BL21(DE3)
BL21 DE3
PLASMID
pET21b
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2006-06-06
1
1
2008-04-30
1
2
2011-07-13
1
3
2021-10-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
N
RCSB
Y
RCSB
2005-07-01
REL
REL
Proton chemical shifts submitted with this deposition were referenced to TSP at 0.00 ppm. However, we should add a cautionary note that this referencing led to an unusually high value for the water signal of 4.966 at 293 K, pH 5.3. We suspect that the TSP resonance is shifted below 0 ppm in our samples, possibly as much as -0.15 ppm. In our view, this is probably due to some transient interaction of the standard with the protein.
all structures compatible with experimental restraints; structures chosen had the lowest energies and/or best agreement to J(NHB) data not used in explicit restraints
40
20
3D_15N-separated_NOESY
HNHA
HNHB
HSQC (amide hydrogen exchange)
3D_13C-separated_NOESY
2D NOESY
2D NOESY
2D NOESY
2D NOESY
no salt added
5.3
ambient
293
K
no salt added
6.1
ambient
293
K
no salt added
6.1
ambient
298
K
40 structures were calculated using 838 noe-derived restraints, 14 hydrogen bond distance restraints, 50 phi angle restraints and 17 chi1 angle restraints. All 40 calculations converged to structures with no noe violations > 0.5 angstroms and no dihedral angle restraint violations >5 degrees. 14 of the 40 structures were discarded based on incompatibility of the rotamer of val 55 with a small J(HNHB) coupling constant, though no explicit restraint on the chi1 angle was included in the calculation. Of the 26 remaining structures, the 6 with the highest energy were discarded. In addition to having high energies, these 6 structures showed unusual conformations, particularly in turn regions, that were unreasonable and in strong disagreement with previously published structures of lambda Cro variants. The final ensemble contains 20 members. The ordered region of the protein extends from approximately residue 3 to residue 55. Pairwise RMSDs for the ordered region were 0.66 A (backbone atoms) and 1.29 A (all heavy atoms). None of the backbone angles in the ordered region of any ensemble member fell outside the most favorable and additionally allowed regions of a ramachandran plot.
simulated annealing
1
closest to the average
2.5 mM lambda Cro A33W/F58D/Y26Q U-13C, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP
90% H2O/10% D2O
5 mM lambda Cro A33W/F58D/Y26Q U-15N, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP
90% H2O/10% D2O
5 mM lambda Cro A33W/F58D/Y26Q unlabelled, 50mM Na-phosphate, 90% H2O, 10% D2O, 0.01% sodium azide, 1 mM TSP
90% H2O/10% D2O
5 mM lambda Cro A33W/F58D/Y26Q U-15N, 50mM Na-phosphate, 100% D2O, 0.01% sodium azide, 1 mM TSP
100% D2O
Bruker
collection
XwinNMR
3.1
Frank Delaglio, Stephan Grzesiek, Ad Bax, Guang Zhu, Geerten Vuister, John Pfeifer
processing
NMRPipe
1.8
Bruce Johnston
data analysis
NMRView
4.1.3
structure solution
CNS
1.1
refinement
CNS
1.1
600
Bruker
DRX
MET
1
n
1
MET
1
A
GLU
2
n
2
GLU
2
A
GLN
3
n
3
GLN
3
A
ARG
4
n
4
ARG
4
A
ILE
5
n
5
ILE
5
A
THR
6
n
6
THR
6
A
LEU
7
n
7
LEU
7
A
LYS
8
n
8
LYS
8
A
ASP
9
n
9
ASP
9
A
TYR
10
n
10
TYR
10
A
ALA
11
n
11
ALA
11
A
MET
12
n
12
MET
12
A
ARG
13
n
13
ARG
13
A
PHE
14
n
14
PHE
14
A
GLY
15
n
15
GLY
15
A
GLN
16
n
16
GLN
16
A
THR
17
n
17
THR
17
A
LYS
18
n
18
LYS
18
A
THR
19
n
19
THR
19
A
ALA
20
n
20
ALA
20
A
LYS
21
n
21
LYS
21
A
ASP
22
n
22
ASP
22
A
LEU
23
n
23
LEU
23
A
GLY
24
n
24
GLY
24
A
VAL
25
n
25
VAL
25
A
GLN
26
n
26
GLN
26
A
GLN
27
n
27
GLN
27
A
SER
28
n
28
SER
28
A
ALA
29
n
29
ALA
29
A
ILE
30
n
30
ILE
30
A
ASN
31
n
31
ASN
31
A
LYS
32
n
32
LYS
32
A
TRP
33
n
33
TRP
33
A
ILE
34
n
34
ILE
34
A
HIS
35
n
35
HIS
35
A
ALA
36
n
36
ALA
36
A
GLY
37
n
37
GLY
37
A
ARG
38
n
38
ARG
38
A
LYS
39
n
39
LYS
39
A
ILE
40
n
40
ILE
40
A
PHE
41
n
41
PHE
41
A
LEU
42
n
42
LEU
42
A
THR
43
n
43
THR
43
A
ILE
44
n
44
ILE
44
A
ASN
45
n
45
ASN
45
A
ALA
46
n
46
ALA
46
A
ASP
47
n
47
ASP
47
A
GLY
48
n
48
GLY
48
A
SER
49
n
49
SER
49
A
VAL
50
n
50
VAL
50
A
TYR
51
n
51
TYR
51
A
ALA
52
n
52
ALA
52
A
GLU
53
n
53
GLU
53
A
GLU
54
n
54
GLU
54
A
VAL
55
n
55
VAL
55
A
LYS
56
n
56
LYS
56
A
PRO
57
n
57
PRO
57
A
ASP
58
n
58
ASP
58
A
PRO
59
n
59
PRO
59
A
SER
60
n
60
SER
60
A
ASN
61
n
61
ASN
61
A
LYS
62
n
62
LYS
62
A
LYS
63
n
63
LYS
63
A
THR
64
n
64
THR
64
A
THR
65
n
65
THR
65
A
ALA
66
n
66
ALA
66
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
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
ILE
5
A
N
ILE
5
A
O
LEU
42
A
O
LEU
42
A
N
PHE
41
A
N
PHE
41
A
O
GLU
53
A
O
GLU
53
1
A
PRO
57
-57.27
-161.69
2
A
GLU
2
60.62
87.26
2
A
GLN
3
-97.82
39.01
2
A
LYS
39
-68.23
76.41
2
A
LYS
62
-79.98
-168.79
2
A
THR
64
-101.85
53.54
3
A
PRO
59
-55.08
87.82
3
A
THR
65
-148.04
32.81
4
A
GLU
2
61.42
169.24
4
A
GLN
3
-147.96
39.66
4
A
ARG
13
-90.15
-69.07
4
A
LYS
39
-66.04
87.84
4
A
PRO
59
-65.31
65.15
4
A
SER
60
56.03
89.71
5
A
GLU
2
62.11
65.73
5
A
GLN
3
-96.15
44.42
5
A
ARG
13
-90.06
-72.49
5
A
PRO
59
-68.32
67.57
5
A
LYS
62
-105.89
-61.08
6
A
GLN
3
-98.48
37.32
6
A
ARG
13
-90.08
-63.84
6
A
PRO
57
-71.95
-168.23
6
A
SER
60
-176.71
-40.35
6
A
LYS
63
-146.29
44.63
7
A
SER
60
-155.25
-66.56
8
A
GLU
2
-73.22
-169.79
8
A
ARG
13
-84.66
-70.26
8
A
LYS
56
-150.60
78.83
8
A
ASP
58
49.39
71.65
8
A
PRO
59
-56.12
86.42
8
A
SER
60
-162.73
86.53
8
A
LYS
62
-133.13
-43.02
9
A
ASP
58
-160.26
79.07
9
A
LYS
62
-131.22
-67.81
10
A
ARG
13
-90.09
-70.44
10
A
SER
60
-157.78
31.22
10
A
LYS
62
-144.17
37.38
10
A
THR
65
-98.21
-66.44
11
A
GLU
2
62.63
118.97
11
A
ARG
13
-90.06
-68.87
11
A
LYS
39
-63.18
84.10
11
A
SER
60
-170.56
78.03
11
A
LYS
62
-158.44
-45.59
13
A
GLU
2
60.64
170.34
13
A
ARG
13
-90.02
-70.19
13
A
PRO
57
-73.16
-169.31
13
A
PRO
59
-67.96
87.31
13
A
SER
60
-90.19
54.18
14
A
GLN
3
-156.97
37.23
14
A
ARG
13
-90.04
-60.67
14
A
PRO
59
-68.36
78.44
14
A
LYS
62
-146.17
-48.13
15
A
PRO
59
-60.02
-150.31
15
A
ASN
61
-160.07
56.07
15
A
LYS
63
-158.19
-46.04
16
A
GLN
3
-152.30
39.55
16
A
PRO
57
-69.76
-167.62
16
A
ASP
58
-116.54
64.61
16
A
THR
65
-150.19
-47.15
17
A
LYS
39
-63.34
87.26
17
A
PRO
59
-43.64
94.31
17
A
ASN
61
-79.79
-166.34
17
A
THR
65
-140.66
31.34
18
A
GLU
2
-168.30
117.75
18
A
ARG
13
-90.04
-70.02
18
A
SER
60
-142.17
-58.10
18
A
LYS
62
-143.34
-58.76
18
A
LYS
63
-160.07
97.19
19
A
GLU
2
-154.83
56.07
19
A
GLN
3
-97.46
38.97
19
A
PRO
59
-62.10
76.06
19
A
SER
60
52.65
83.70
20
A
GLN
3
-159.22
36.78
20
A
ARG
13
-90.06
-66.93
Solution structure of a stably monomeric mutant of lambda Cro produced by substitutions in the ball-and-socket interface
1
N
N
A
LEU
7
A
LEU
7
HELX_P
A
PHE
14
A
PHE
14
1
1
8
A
GLY
15
A
GLY
15
HELX_P
A
GLY
24
A
GLY
24
1
2
10
A
GLN
26
A
GLN
26
HELX_P
A
ALA
36
A
ALA
36
1
3
11
VIRAL PROTEIN
helix-turn-helix, monomer, ball-and-socket, VIRAL PROTEIN
RCRO_LAMBD
UNP
1
1
P03040
1
66
2A63
1
66
P03040
A
1
1
66
1
TYR
engineered mutation
GLN
26
2A63
A
P03040
UNP
26
26
1
ALA
engineered mutation
TRP
33
2A63
A
P03040
UNP
33
33
1
PHE
engineered mutation
ASP
58
2A63
A
P03040
UNP
58
58
3
anti-parallel
anti-parallel
A
ARG
4
A
ARG
4
A
THR
6
A
THR
6
A
ILE
40
A
ILE
40
A
ILE
44
A
ILE
44
A
VAL
50
A
VAL
50
A
GLU
54
A
GLU
54