0.025537
0.000000
0.000000
0.000000
0.017344
0.000000
0.000000
0.000000
0.010716
0.00000
0.00000
0.00000
Lee, S.
Antony, L.
Hartmann, R.
Knaus, K.J.
Surewicz, K.
Surewicz, W.K.
Yee, V.C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.00
90.00
90.00
39.159
57.656
93.315
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
Cd 2
112.411
CADMIUM ION
non-polymer
Cl -1
35.453
CHLORIDE ION
non-polymer
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
UK
Embo J.
EMJODG
0897
0261-4189
29
251
262
10.1038/emboj.2009.333
19927125
Conformational diversity in prion protein variants influences intermolecular beta-sheet formation.
2010
10.2210/pdb3hjx/pdb
pdb_00003hjx
100
1
2006-08-07
SINGLE WAVELENGTH
M
x-ray
1
0.9198
1.0
19-BM
APS
0.9198
SYNCHROTRON
APS BEAMLINE 19-BM
12644.971
Major prion protein
UNP RESIDUES 90-231
D178N
1
man
polymer
112.411
CADMIUM ION
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
55
nat
water
PrP, PrP27-30, PrP33-35C, ASCR
no
no
GGYVLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHNCVNITIKQHTVTTTTKGENFTETDVKM
MERVVEQMCITQYERESQAYYQRGSS
GGYVLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHNCVNITIKQHTVTTTTKGENFTETDVKM
MERVVEQMCITQYERESQAYYQRGSS
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
human
sample
PRNP, PRIP, PRP
9606
Homo sapiens
562
Escherichia coli
1
2.08
40.94
VAPOR DIFFUSION, SITTING DROP
7.0
0.1M Tris (pH 7.0), 2.0 M NaCl and 5 mM CdCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
software
database_2
pdbx_struct_conn_angle
pdbx_struct_special_symmetry
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Refinement description
Database references
Derived calculations
1
0
2010-01-12
1
1
2011-07-13
1
2
2017-11-01
1
3
2021-10-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_alt_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_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr2_label_alt_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_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_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2009-05-22
REL
REL
CD
CADMIUM ION
CL
CHLORIDE ION
HOH
water
THE COMPLETE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZATION WAS:
GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYVLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSS. HOWEVER ACCORDING TO THE AUTHORS THERE IS A REASONABLE CHANCE THAT THE CRYSTAL
CONTAINS A PROTEOLYZED VERSION. ONLY THE RESIDUES OBSERVED IN THE EXPERIMENT WERE INCLUDED IN THE SEQRES RECORDS.
CD
300
2
CD
CD
300
A
CL
301
3
CL
CL
301
A
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
304
4
HOH
HOH
304
A
HOH
305
4
HOH
HOH
305
A
HOH
306
4
HOH
HOH
306
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
309
4
HOH
HOH
309
A
HOH
310
4
HOH
HOH
310
A
HOH
311
4
HOH
HOH
311
A
HOH
312
4
HOH
HOH
312
A
HOH
313
4
HOH
HOH
313
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
319
4
HOH
HOH
319
A
HOH
320
4
HOH
HOH
320
A
HOH
321
4
HOH
HOH
321
A
HOH
322
4
HOH
HOH
322
A
HOH
323
4
HOH
HOH
323
A
HOH
324
4
HOH
HOH
324
A
HOH
325
4
HOH
HOH
325
A
HOH
326
4
HOH
HOH
326
A
HOH
327
4
HOH
HOH
327
A
HOH
328
4
HOH
HOH
328
A
HOH
329
4
HOH
HOH
329
A
HOH
330
4
HOH
HOH
330
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
336
4
HOH
HOH
336
A
HOH
337
4
HOH
HOH
337
A
HOH
338
4
HOH
HOH
338
A
HOH
339
4
HOH
HOH
339
A
HOH
340
4
HOH
HOH
340
A
HOH
341
4
HOH
HOH
341
A
HOH
342
4
HOH
HOH
342
A
HOH
343
4
HOH
HOH
343
A
HOH
344
4
HOH
HOH
344
A
HOH
345
4
HOH
HOH
345
A
HOH
346
4
HOH
HOH
346
A
HOH
347
4
HOH
HOH
347
A
HOH
348
4
HOH
HOH
348
A
HOH
349
4
HOH
HOH
349
A
HOH
350
4
HOH
HOH
350
A
HOH
351
4
HOH
HOH
351
A
HOH
352
4
HOH
HOH
352
A
HOH
353
4
HOH
HOH
353
A
HOH
354
4
HOH
HOH
354
A
HOH
355
4
HOH
HOH
355
A
HOH
356
4
HOH
HOH
356
A
GLY
126
n
1
GLY
126
A
GLY
127
n
2
GLY
127
A
TYR
128
n
3
TYR
128
A
VAL
129
n
4
VAL
129
A
LEU
130
n
5
LEU
130
A
GLY
131
n
6
GLY
131
A
SER
132
n
7
SER
132
A
ALA
133
n
8
ALA
133
A
MET
134
n
9
MET
134
A
SER
135
n
10
SER
135
A
ARG
136
n
11
ARG
136
A
PRO
137
n
12
PRO
137
A
ILE
138
n
13
ILE
138
A
ILE
139
n
14
ILE
139
A
HIS
140
n
15
HIS
140
A
PHE
141
n
16
PHE
141
A
GLY
142
n
17
GLY
142
A
SER
143
n
18
SER
143
A
ASP
144
n
19
ASP
144
A
TYR
145
n
20
TYR
145
A
GLU
146
n
21
GLU
146
A
ASP
147
n
22
ASP
147
A
ARG
148
n
23
ARG
148
A
TYR
149
n
24
TYR
149
A
TYR
150
n
25
TYR
150
A
ARG
151
n
26
ARG
151
A
GLU
152
n
27
GLU
152
A
ASN
153
n
28
ASN
153
A
MET
154
n
29
MET
154
A
HIS
155
n
30
HIS
155
A
ARG
156
n
31
ARG
156
A
TYR
157
n
32
TYR
157
A
PRO
158
n
33
PRO
158
A
ASN
159
n
34
ASN
159
A
GLN
160
n
35
GLN
160
A
VAL
161
n
36
VAL
161
A
TYR
162
n
37
TYR
162
A
TYR
163
n
38
TYR
163
A
ARG
164
n
39
ARG
164
A
PRO
165
n
40
PRO
165
A
MET
166
n
41
MET
166
A
ASP
167
n
42
ASP
167
A
GLU
168
n
43
GLU
168
A
TYR
169
n
44
TYR
169
A
SER
170
n
45
SER
170
A
ASN
171
n
46
ASN
171
A
GLN
172
n
47
GLN
172
A
ASN
173
n
48
ASN
173
A
ASN
174
n
49
ASN
174
A
PHE
175
n
50
PHE
175
A
VAL
176
n
51
VAL
176
A
HIS
177
n
52
HIS
177
A
ASN
178
n
53
ASN
178
A
CYS
179
n
54
CYS
179
A
VAL
180
n
55
VAL
180
A
ASN
181
n
56
ASN
181
A
ILE
182
n
57
ILE
182
A
THR
183
n
58
THR
183
A
ILE
184
n
59
ILE
184
A
LYS
185
n
60
LYS
185
A
GLN
186
n
61
GLN
186
A
HIS
187
n
62
HIS
187
A
THR
188
n
63
THR
188
A
VAL
189
n
64
VAL
189
A
THR
190
n
65
THR
190
A
THR
191
n
66
THR
191
A
THR
192
n
67
THR
192
A
n
68
193
A
n
69
194
A
n
70
195
A
GLU
196
n
71
GLU
196
A
ASN
197
n
72
ASN
197
A
PHE
198
n
73
PHE
198
A
THR
199
n
74
THR
199
A
GLU
200
n
75
GLU
200
A
THR
201
n
76
THR
201
A
ASP
202
n
77
ASP
202
A
VAL
203
n
78
VAL
203
A
LYS
204
n
79
LYS
204
A
MET
205
n
80
MET
205
A
MET
206
n
81
MET
206
A
GLU
207
n
82
GLU
207
A
ARG
208
n
83
ARG
208
A
VAL
209
n
84
VAL
209
A
VAL
210
n
85
VAL
210
A
GLU
211
n
86
GLU
211
A
GLN
212
n
87
GLN
212
A
MET
213
n
88
MET
213
A
CYS
214
n
89
CYS
214
A
ILE
215
n
90
ILE
215
A
THR
216
n
91
THR
216
A
GLN
217
n
92
GLN
217
A
TYR
218
n
93
TYR
218
A
GLU
219
n
94
GLU
219
A
ARG
220
n
95
ARG
220
A
GLU
221
n
96
GLU
221
A
SER
222
n
97
SER
222
A
GLN
223
n
98
GLN
223
A
n
99
224
A
n
100
225
A
n
101
226
A
n
102
227
A
n
103
228
A
n
104
229
A
n
105
230
A
n
106
231
A
software_defined_assembly
PISA
2
dimeric
software_defined_assembly
PISA
2
dimeric
1080
-42
11710
1900
-16
10630
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
A
B
CD
CD
1_555
A
ASP
147
A
OD1
ASP
22
1_555
149.2
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
A
B
CD
CD
1_555
A
ASP
147
A
OD2
ASP
22
1_555
107.2
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
A
B
CD
CD
1_555
A
ASP
147
A
OD2
ASP
22
1_555
55.0
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
A
B
CD
CD
1_555
A
HOH
350
D
O
HOH
1_555
100.1
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
A
B
CD
CD
1_555
A
HOH
350
D
O
HOH
1_555
99.6
A
ASP
147
A
OD2
ASP
22
1_555
A
CD
300
A
B
CD
CD
1_555
A
HOH
350
D
O
HOH
1_555
77.2
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
B
B
CD
CD
1_555
A
ASP
147
A
OD1
ASP
22
1_555
135.0
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
B
B
CD
CD
1_555
A
ASP
147
A
OD2
ASP
22
1_555
93.4
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
B
B
CD
CD
1_555
A
ASP
147
A
OD2
ASP
22
1_555
49.7
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
B
B
CD
CD
1_555
A
HOH
354
B
D
O
HOH
1_555
104.2
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
B
B
CD
CD
1_555
A
HOH
354
B
D
O
HOH
1_555
118.3
A
ASP
147
A
OD2
ASP
22
1_555
A
CD
300
B
B
CD
CD
1_555
A
HOH
354
B
D
O
HOH
1_555
159.0
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
6_775
-x+2,-y+5/2,z
crystal symmetry operation
78.3180000000
144.1400000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
8_576
x,-y+2,-z+3/2
crystal symmetry operation
0.0000000000
115.3120000000
139.9725000000
A
N
VAL
129
A
N
VAL
4
A
O
TYR
163
A
O
TYR
38
1
A
CL
301
C
CL
1
A
THR
193
A
THR
68
1
Y
1
A
LYS
194
A
LYS
69
1
Y
1
A
GLY
195
A
GLY
70
1
Y
1
A
ALA
224
A
ALA
99
1
Y
1
A
TYR
225
A
TYR
100
1
Y
1
A
TYR
226
A
TYR
101
1
Y
1
A
GLN
227
A
GLN
102
1
Y
1
A
ARG
228
A
ARG
103
1
Y
1
A
GLY
229
A
GLY
104
1
Y
1
A
SER
230
A
SER
105
1
Y
1
A
SER
231
A
SER
106
1
Y
1
A
A
O
N
MET
GLU
166
168
1.95
1
A
A
GLU
TYR
168
169
-113.20
1
-12.91
1.90
113.40
100.49
A
A
A
CA
CB
CG
TYR
TYR
TYR
169
169
169
N
1
A
A
ND1
CD
HIS
CD
177
300
1.86
A
1_555
8_576
1
A
ASP
167
-55.23
48.70
1
A
TYR
169
-2.17
73.92
1
A
ASN
197
52.09
-136.78
1
A
SER
222
-43.49
109.91
33.288
-0.01
0.00
0.00
0.01
0.00
0.00
0.940
0.911
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.26630
0.20524
0.20800
2.00
27.38
341
7061
4.6
100.00
1.00
0.50
4.583
0.128
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.203
0.189
0.80
0.80
1.40
MAXIMUM LIKELIHOOD
MASK
2.00
27.38
56
858
3
0
799
0.012
0.021
818
1.464
1.919
1105
9.008
5.000
93
37.771
24.000
50
15.159
15.000
140
20.648
15.000
7
0.108
0.200
113
0.008
0.021
648
1.142
1.500
473
2.112
2.000
773
2.484
3.000
345
3.985
4.500
332
0.338
0.247
2.053
28
504
20
100.00
2.000
50.000
3HJX
7405
0.067
1
23.186
5.000
99.500
0.471
2.00
2.07
4.70
99.90
0.347
2.07
2.15
5.10
100.00
0.269
2.15
2.25
5.10
100.00
0.210
2.25
2.37
5.10
100.00
0.172
2.37
2.52
5.10
100.00
0.128
2.52
2.71
5.10
99.90
0.093
2.71
2.99
5.10
99.90
0.051
2.99
3.42
5.00
99.50
0.033
3.42
4.31
5.00
99.30
0.029
4.31
50.00
4.90
97.30
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0066
data extraction
PDB
help@deposit.rcsb.org
June 11, 2008
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.005
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
phasing
EPMR
Human prion protein variant D178N with V129
1
N
N
2
N
N
3
N
N
4
N
N
A
SER
143
A
SER
18
HELX_P
A
MET
154
A
MET
29
1
1
12
A
HIS
155
A
HIS
30
HELX_P
A
TYR
157
A
TYR
32
5
2
3
A
ASN
171
A
ASN
46
HELX_P
A
THR
191
A
THR
66
1
3
21
A
THR
199
A
THR
74
HELX_P
A
SER
222
A
SER
97
1
4
24
disulf
2.039
A
CYS
179
A
SG
CYS
54
1_555
A
CYS
214
A
SG
CYS
89
1_555
metalc
2.388
A
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.516
B
A
HIS
140
A
ND1
HIS
15
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.376
A
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.455
B
A
ASP
147
A
OD1
ASP
22
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.300
A
A
ASP
147
A
OD2
ASP
22
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.666
B
A
ASP
147
A
OD2
ASP
22
1_555
A
CD
300
B
CD
CD
1_555
metalc
2.446
A
A
CD
300
B
CD
CD
1_555
A
HOH
350
D
O
HOH
1_555
metalc
2.407
B
B
A
CD
300
B
CD
CD
1_555
A
HOH
354
D
O
HOH
1_555
MEMBRANE PROTEIN
Prion protein, Cell membrane, Disease mutation, Disulfide bond, Glycoprotein, Golgi apparatus, GPI-anchor, Lipoprotein, Membrane, Polymorphism, Prion, MEMBRANE PROTEIN
PRIO_HUMAN
UNP
1
126
P04156
GGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKM
MERVVEQMCITQYERESQAYYQRGSS
126
231
3HJX
126
231
P04156
A
1
1
106
1
MET
variant
VAL
129
3HJX
A
P04156
UNP
129
4
1
ASP
engineered mutation
ASN
178
3HJX
A
P04156
UNP
178
53
2
anti-parallel
A
VAL
129
A
VAL
4
A
LEU
130
A
LEU
5
A
TYR
162
A
TYR
37
A
TYR
163
A
TYR
38
BINDING SITE FOR RESIDUE CD A 300
A
CD
300
Software
6
BINDING SITE FOR RESIDUE CL A 301
A
CL
301
Software
1
A
HIS
140
A
HIS
15
6
1_555
A
ASP
147
A
ASP
22
6
1_555
A
HIS
177
A
HIS
52
6
8_576
A
HOH
302
D
HOH
6
1_555
A
HOH
350
D
HOH
6
1_555
A
HOH
354
D
HOH
6
1_555
A
ASN
173
A
ASN
48
1
6_775
24
I 21 21 21