0.032765
0.000000
0.009210
0.000000
0.026042
0.000000
0.000000
0.000000
0.019485
0.00000
0.00000
0.00000
Schultz, L.W.
Quirk, D.J.
Raines, R.T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.00
105.70
90.00
30.520
38.400
53.310
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 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
Biochemistry
BICHAW
0033
0006-2960
37
8886
8898
10.1021/bi972766q
9636030
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
1998
10.2210/pdb3rsd/pdb
pdb_00003rsd
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
277
1
LONG MIRRORS
AREA DETECTOR
1995-08-28
SIEMENS
NI FILTER
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RUH2R
13707.342
RIBONUCLEASE A
3.1.27.5
D121N
1
man
polymer
18.015
water
100
nat
water
no
no
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMS
ITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFNASV
KETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADVQAVCSQKNVACKNGQTNCYQSYSTMS
ITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFNASV
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
cattle
Bos
Escherichia
Escherichia coli
sample
BL21
9913
PANCREAS
Bos taurus
INCLUSION BODIES
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PET-22
PBXR
1
2.19
60
batch method
5.2
LYOPHILIZED D121N RNASE A WAS DISSOLVED IN UNBUFFERED WATER TO A CONCENTRATION OF 60MG/ ML. CRYSTALLIZATION WAS PERFORMED IN SMALL SILICONIZED TUBES USING THE BATCH METHOD. A SOLUTION (25UL) OF THE ENZYME WAS MIXED WITH AN EQUAL VOLUME OF 95% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.10 M MES BUFFER, PH 5.2. CRYSTALS APPEARED WITHIN SEVERAL MONTHS., batch method
database_2
struct_ref_seq_dif
pdbx_initial_refinement_model
repository
Initial release
Version format compliance
Version format compliance
Database references
Refinement description
1
0
1998-07-15
1
1
2008-03-25
1
2
2011-07-13
1
3
2021-11-03
1
4
2023-08-09
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
BNL
1998-02-05
REL
HOH
water
1RPH
PDB ENTRY 1RPH
PDB
experimental model
HOH
125
2
HOH
HOH
125
A
HOH
126
2
HOH
HOH
126
A
HOH
127
2
HOH
HOH
127
A
HOH
128
2
HOH
HOH
128
A
HOH
129
2
HOH
HOH
129
A
HOH
130
2
HOH
HOH
130
A
HOH
131
2
HOH
HOH
131
A
HOH
132
2
HOH
HOH
132
A
HOH
133
2
HOH
HOH
133
A
HOH
134
2
HOH
HOH
134
A
HOH
135
2
HOH
HOH
135
A
HOH
136
2
HOH
HOH
136
A
HOH
137
2
HOH
HOH
137
A
HOH
138
2
HOH
HOH
138
A
HOH
139
2
HOH
HOH
139
A
HOH
140
2
HOH
HOH
140
A
HOH
141
2
HOH
HOH
141
A
HOH
142
2
HOH
HOH
142
A
HOH
143
2
HOH
HOH
143
A
HOH
144
2
HOH
HOH
144
A
HOH
145
2
HOH
HOH
145
A
HOH
146
2
HOH
HOH
146
A
HOH
147
2
HOH
HOH
147
A
HOH
148
2
HOH
HOH
148
A
HOH
149
2
HOH
HOH
149
A
HOH
150
2
HOH
HOH
150
A
HOH
151
2
HOH
HOH
151
A
HOH
152
2
HOH
HOH
152
A
HOH
153
2
HOH
HOH
153
A
HOH
154
2
HOH
HOH
154
A
HOH
155
2
HOH
HOH
155
A
HOH
156
2
HOH
HOH
156
A
HOH
157
2
HOH
HOH
157
A
HOH
158
2
HOH
HOH
158
A
HOH
159
2
HOH
HOH
159
A
HOH
160
2
HOH
HOH
160
A
HOH
161
2
HOH
HOH
161
A
HOH
162
2
HOH
HOH
162
A
HOH
163
2
HOH
HOH
163
A
HOH
164
2
HOH
HOH
164
A
HOH
165
2
HOH
HOH
165
A
HOH
166
2
HOH
HOH
166
A
HOH
167
2
HOH
HOH
167
A
HOH
168
2
HOH
HOH
168
A
HOH
169
2
HOH
HOH
169
A
HOH
170
2
HOH
HOH
170
A
HOH
171
2
HOH
HOH
171
A
HOH
172
2
HOH
HOH
172
A
HOH
173
2
HOH
HOH
173
A
HOH
174
2
HOH
HOH
174
A
HOH
175
2
HOH
HOH
175
A
HOH
176
2
HOH
HOH
176
A
HOH
177
2
HOH
HOH
177
A
HOH
178
2
HOH
HOH
178
A
HOH
179
2
HOH
HOH
179
A
HOH
180
2
HOH
HOH
180
A
HOH
181
2
HOH
HOH
181
A
HOH
182
2
HOH
HOH
182
A
HOH
183
2
HOH
HOH
183
A
HOH
184
2
HOH
HOH
184
A
HOH
185
2
HOH
HOH
185
A
HOH
186
2
HOH
HOH
186
A
HOH
187
2
HOH
HOH
187
A
HOH
188
2
HOH
HOH
188
A
HOH
189
2
HOH
HOH
189
A
HOH
190
2
HOH
HOH
190
A
HOH
191
2
HOH
HOH
191
A
HOH
192
2
HOH
HOH
192
A
HOH
193
2
HOH
HOH
193
A
HOH
194
2
HOH
HOH
194
A
HOH
195
2
HOH
HOH
195
A
HOH
196
2
HOH
HOH
196
A
HOH
197
2
HOH
HOH
197
A
HOH
198
2
HOH
HOH
198
A
HOH
199
2
HOH
HOH
199
A
HOH
200
2
HOH
HOH
200
A
HOH
201
2
HOH
HOH
201
A
HOH
202
2
HOH
HOH
202
A
HOH
203
2
HOH
HOH
203
A
HOH
204
2
HOH
HOH
204
A
HOH
205
2
HOH
HOH
205
A
HOH
206
2
HOH
HOH
206
A
HOH
207
2
HOH
HOH
207
A
HOH
208
2
HOH
HOH
208
A
HOH
209
2
HOH
HOH
209
A
HOH
210
2
HOH
HOH
210
A
HOH
211
2
HOH
HOH
211
A
HOH
212
2
HOH
HOH
212
A
HOH
213
2
HOH
HOH
213
A
HOH
214
2
HOH
HOH
214
A
HOH
215
2
HOH
HOH
215
A
HOH
216
2
HOH
HOH
216
A
HOH
217
2
HOH
HOH
217
A
HOH
218
2
HOH
HOH
218
A
HOH
219
2
HOH
HOH
219
A
HOH
220
2
HOH
HOH
220
A
HOH
221
2
HOH
HOH
221
A
HOH
222
2
HOH
HOH
222
A
HOH
223
2
HOH
HOH
223
A
HOH
224
2
HOH
HOH
224
A
LYS
1
n
1
LYS
1
A
GLU
2
n
2
GLU
2
A
THR
3
n
3
THR
3
A
ALA
4
n
4
ALA
4
A
ALA
5
n
5
ALA
5
A
ALA
6
n
6
ALA
6
A
LYS
7
n
7
LYS
7
A
PHE
8
n
8
PHE
8
A
GLU
9
n
9
GLU
9
A
ARG
10
n
10
ARG
10
A
GLN
11
n
11
GLN
11
A
HIS
12
n
12
HIS
12
A
MET
13
n
13
MET
13
A
ASP
14
n
14
ASP
14
A
SER
15
n
15
SER
15
A
SER
16
n
16
SER
16
A
THR
17
n
17
THR
17
A
SER
18
n
18
SER
18
A
ALA
19
n
19
ALA
19
A
ALA
20
n
20
ALA
20
A
SER
21
n
21
SER
21
A
SER
22
n
22
SER
22
A
SER
23
n
23
SER
23
A
ASN
24
n
24
ASN
24
A
TYR
25
n
25
TYR
25
A
CYS
26
n
26
CYS
26
A
ASN
27
n
27
ASN
27
A
GLN
28
n
28
GLN
28
A
MET
29
n
29
MET
29
A
MET
30
n
30
MET
30
A
LYS
31
n
31
LYS
31
A
SER
32
n
32
SER
32
A
ARG
33
n
33
ARG
33
A
ASN
34
n
34
ASN
34
A
LEU
35
n
35
LEU
35
A
THR
36
n
36
THR
36
A
LYS
37
n
37
LYS
37
A
ASP
38
n
38
ASP
38
A
ARG
39
n
39
ARG
39
A
CYS
40
n
40
CYS
40
A
LYS
41
n
41
LYS
41
A
PRO
42
n
42
PRO
42
A
VAL
43
n
43
VAL
43
A
ASN
44
n
44
ASN
44
A
THR
45
n
45
THR
45
A
PHE
46
n
46
PHE
46
A
VAL
47
n
47
VAL
47
A
HIS
48
n
48
HIS
48
A
GLU
49
n
49
GLU
49
A
SER
50
n
50
SER
50
A
LEU
51
n
51
LEU
51
A
ALA
52
n
52
ALA
52
A
ASP
53
n
53
ASP
53
A
VAL
54
n
54
VAL
54
A
GLN
55
n
55
GLN
55
A
ALA
56
n
56
ALA
56
A
VAL
57
n
57
VAL
57
A
CYS
58
n
58
CYS
58
A
SER
59
n
59
SER
59
A
GLN
60
n
60
GLN
60
A
LYS
61
n
61
LYS
61
A
ASN
62
n
62
ASN
62
A
VAL
63
n
63
VAL
63
A
ALA
64
n
64
ALA
64
A
CYS
65
n
65
CYS
65
A
LYS
66
n
66
LYS
66
A
ASN
67
n
67
ASN
67
A
GLY
68
n
68
GLY
68
A
GLN
69
n
69
GLN
69
A
THR
70
n
70
THR
70
A
ASN
71
n
71
ASN
71
A
CYS
72
n
72
CYS
72
A
TYR
73
n
73
TYR
73
A
GLN
74
n
74
GLN
74
A
SER
75
n
75
SER
75
A
TYR
76
n
76
TYR
76
A
SER
77
n
77
SER
77
A
THR
78
n
78
THR
78
A
MET
79
n
79
MET
79
A
SER
80
n
80
SER
80
A
ILE
81
n
81
ILE
81
A
THR
82
n
82
THR
82
A
ASP
83
n
83
ASP
83
A
CYS
84
n
84
CYS
84
A
ARG
85
n
85
ARG
85
A
GLU
86
n
86
GLU
86
A
THR
87
n
87
THR
87
A
GLY
88
n
88
GLY
88
A
SER
89
n
89
SER
89
A
SER
90
n
90
SER
90
A
LYS
91
n
91
LYS
91
A
TYR
92
n
92
TYR
92
A
PRO
93
n
93
PRO
93
A
ASN
94
n
94
ASN
94
A
CYS
95
n
95
CYS
95
A
ALA
96
n
96
ALA
96
A
TYR
97
n
97
TYR
97
A
LYS
98
n
98
LYS
98
A
THR
99
n
99
THR
99
A
THR
100
n
100
THR
100
A
GLN
101
n
101
GLN
101
A
ALA
102
n
102
ALA
102
A
ASN
103
n
103
ASN
103
A
LYS
104
n
104
LYS
104
A
HIS
105
n
105
HIS
105
A
ILE
106
n
106
ILE
106
A
ILE
107
n
107
ILE
107
A
VAL
108
n
108
VAL
108
A
ALA
109
n
109
ALA
109
A
CYS
110
n
110
CYS
110
A
GLU
111
n
111
GLU
111
A
GLY
112
n
112
GLY
112
A
ASN
113
n
113
ASN
113
A
PRO
114
n
114
PRO
114
A
TYR
115
n
115
TYR
115
A
VAL
116
n
116
VAL
116
A
PRO
117
n
117
PRO
117
A
VAL
118
n
118
VAL
118
A
HIS
119
n
119
HIS
119
A
PHE
120
n
120
PHE
120
A
ASN
121
n
121
ASN
121
A
ALA
122
n
122
ALA
122
A
SER
123
n
123
SER
123
A
VAL
124
n
124
VAL
124
A
0.177
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
PRO
42
A
O
PRO
42
A
N
GLU
86
A
N
GLU
86
A
N
MET
79
A
N
MET
79
A
O
LYS
104
A
O
LYS
104
A
N
LYS
91
A
N
LYS
91
A
O
ASN
94
A
O
ASN
94
A
N
VAL
63
A
N
VAL
63
A
O
CYS
72
A
O
CYS
72
A
N
TYR
73
A
N
TYR
73
A
O
VAL
108
A
O
VAL
108
A
N
GLU
111
A
N
GLU
111
A
O
VAL
116
A
O
VAL
116
A
N
VAL
63
A
N
VAL
63
A
O
CYS
72
A
O
CYS
72
A
N
TYR
73
A
N
TYR
73
A
O
VAL
108
A
O
VAL
108
A
O
HIS
105
A
O
HIS
105
A
N
VAL
124
A
N
VAL
124
1
-6.26
0.90
118.30
112.04
A
A
A
CB
CG
OD2
ASP
ASP
ASP
14
14
14
N
1
-6.30
0.90
118.30
112.00
A
A
A
CB
CG
OD2
ASP
ASP
ASP
83
83
83
N
1
A
A
CD
OE1
GLU
GLU
86
86
0.066
0.011
1.252
1.318
N
1
A
HIS
48
-101.15
67.24
1
A
GLN
60
-97.79
-141.45
0.177
1.6
30.0
15756
15756
88.0
1
TNT BCORREL
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 1RPH
TNT PROTGEO
BABINET SCALING
257
0.75
1.6
30.0
100
1056
0
0
956
0.011
980
5.0
2.15
1323
8.0
17.1
597
0.00
0
0.005
28
25.0
0.009
140
50.0
1.0
0.026
9
50.0
1.6
30.0
3RSD
15756
0.33
0.019
1
31
1.8
88
1.6
1.7
0.057
75
data scaling
XDS
data reduction
XCALIBRE
phasing
AMoRE
refinement
TNT
5E
data reduction
XDS
data scaling
XCALIBRE
STRUCTURE OF THE D121N VARIANT OF RIBONUCLEASE A
1
N
N
2
N
N
A
THR
3
A
THR
3
HELX_P
A
MET
13
A
MET
13
1
H1
11
A
ASN
24
A
ASN
24
HELX_P
A
ASN
34
A
ASN
34
1
H2
11
A
SER
50
A
SER
50
HELX_P
A
GLN
60
A
GLN
60
1
H3
11
disulf
2.054
A
CYS
26
A
SG
CYS
26
1_555
A
CYS
84
A
SG
CYS
84
1_555
disulf
2.011
A
CYS
40
A
SG
CYS
40
1_555
A
CYS
95
A
SG
CYS
95
1_555
disulf
2.001
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
110
A
SG
CYS
110
1_555
disulf
2.029
A
CYS
65
A
SG
CYS
65
1_555
A
CYS
72
A
SG
CYS
72
1_555
HYDROLASE
HYDROLASE, ENDONUCLEASE, RIBONUCLEASE A, SITE-DIRECTED MUTAGENESIS
A
TYR
92
A
TYR
92
1
A
PRO
93
A
PRO
93
5.57
A
ASN
113
A
ASN
113
1
A
PRO
114
A
PRO
114
2.29
RNAS1_BOVIN
UNP
1
1
P61823
MALKSLVLLSLLVLVLLLVRVQPSLGKETAAAKFERQHMDSSTSAASSSNYCNQMMKSRNLTKDRCKPVNTFVHESLADV
QAVCSQKNVACKNGQTNCYQSYSTMSITDCRETGSSKYPNCAYKTTQANKHIIVACEGNPYVPVHFDASV
27
150
3RSD
1
124
P61823
A
1
1
124
1
ASP
engineered mutation
ASN
121
3RSD
A
P61823
UNP
147
121
3
3
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
41
A
LYS
41
A
HIS
48
A
HIS
48
A
MET
79
A
MET
79
A
THR
87
A
THR
87
A
ASN
94
A
ASN
94
A
LYS
104
A
LYS
104
A
LYS
41
A
LYS
41
A
HIS
48
A
HIS
48
A
SER
90
A
SER
90
A
LYS
91
A
LYS
91
A
ASN
94
A
ASN
94
A
LYS
104
A
LYS
104
A
LYS
61
A
LYS
61
A
ALA
64
A
ALA
64
A
ASN
71
A
ASN
71
A
SER
75
A
SER
75
A
HIS
105
A
HIS
105
A
ASN
113
A
ASN
113
A
PRO
114
A
PRO
114
A
HIS
119
A
HIS
119
A
LYS
61
A
LYS
61
A
ALA
64
A
ALA
64
A
ASN
71
A
ASN
71
A
SER
75
A
SER
75
A
HIS
105
A
HIS
105
A
ASN
113
A
ASN
113
A
ASN
121
A
ASN
121
A
VAL
124
A
VAL
124
CATALYZES CLEAVAGE OF THE P-O5' BOND OF A PHOSPHORYL GROUP IN THIS SUBSITE.
Unknown
3
PHOSPHATE BINDING SITE.
Unknown
2
PYRIMIDINE BINDING SITE ON 5' SIDE OF SCISSILE PHOSPHATE.
Unknown
2
PURINE BINDING SITE ON 3' SIDE OF SCISSILE PHOSPHATE.
Unknown
2
A
HIS
12
A
HIS
12
3
1_555
A
HIS
119
A
HIS
119
3
1_555
A
LYS
41
A
LYS
41
3
1_555
A
LYS
7
A
LYS
7
2
1_555
A
ARG
10
A
ARG
10
2
1_555
A
THR
45
A
THR
45
2
1_555
A
ASP
83
A
ASP
83
2
1_555
A
ASN
71
A
ASN
71
2
1_555
A
GLU
111
A
GLU
111
2
1_555
4
P 1 21 1