0.015011
0.008667
0.000000
0.000000
0.017334
0.000000
0.000000
0.000000
0.021517
0.000000
0.000000
0.000000
Nedyalkova, L.
Tong, Y.
Tempel, W.
Zhong, N.
Guan, X.
Landry, R.
Arrowsmith, C.H.
Edwards, A.M.
Bountra, C.
Weigelt, J.
Bochkarev, A.
Park, H.
Structural Genomics Consortium (SGC)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.000
90.000
120.000
66.616
66.616
46.475
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
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
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
UNKNOWN ATOM OR ION
non-polymer
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
TO BE PUBLISHED
0353
Crystal structure of the PDZ domain of MPP7
100
1
100
1
CCD
2010-06-17
ADSC QUANTUM 315
IMAGE PLATE
2010-06-13
RIGAKU RAXIS
SINGLE WAVELENGTH
M
x-ray
1
SINGLE WAVELENGTH
M
x-ray
1
0.97904
1.0
1.5418
1.0
19-ID
APS
0.97904
SYNCHROTRON
APS BEAMLINE 19-ID
1.5418
ROTATING ANODE
RIGAKU FR-E DW
10102.445
MAGUK p55 subfamily member 7
PDZ Domain (UNP residues 135-225)
1
man
polymer
UNKNOWN ATOM OR ION
13
syn
non-polymer
18.015
water
69
nat
water
no
yes
GSDSVKIIRLVKNREPLGATIKKDEQTGAIIVARI(MSE)RGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQS
QGAITFKIIPGSKEETP
GSDSVKIIRLVKNREPLGATIKKDEQTGAIIVARIMRGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQSQGAI
TFKIIPGSKEETP
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
human
sample
MPP7
9606
Homo sapiens
511693
Escherichia coli
BL21-V2R-pRARE2
pET28a-LIC
1
2.95
58.26
VAPOR DIFFUSION, SITTING DROP
7.5
30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 291K
291
Structural Genomics Consortium
SGC
software
repository
Initial release
Version format compliance
Refinement description
1
0
2010-08-04
1
1
2011-07-13
1
2
2017-11-08
Y
RCSB
Y
RCSB
2010-07-26
REL
REL
UNX
UNKNOWN ATOM OR ION
HOH
water
UNX
1
2
UNX
UNX
1
A
UNX
2
2
UNX
UNX
2
A
UNX
3
2
UNX
UNX
3
A
UNX
4
2
UNX
UNX
4
A
UNX
5
2
UNX
UNX
5
A
UNX
6
2
UNX
UNX
6
A
UNX
7
2
UNX
UNX
7
A
UNX
8
2
UNX
UNX
8
A
UNX
9
2
UNX
UNX
9
A
UNX
10
2
UNX
UNX
10
A
UNX
11
2
UNX
UNX
11
A
UNX
12
2
UNX
UNX
12
A
UNX
13
2
UNX
UNX
13
A
HOH
14
3
HOH
HOH
14
A
HOH
15
3
HOH
HOH
15
A
HOH
16
3
HOH
HOH
16
A
HOH
17
3
HOH
HOH
17
A
HOH
18
3
HOH
HOH
18
A
HOH
19
3
HOH
HOH
19
A
HOH
20
3
HOH
HOH
20
A
HOH
21
3
HOH
HOH
21
A
HOH
22
3
HOH
HOH
22
A
HOH
23
3
HOH
HOH
23
A
HOH
24
3
HOH
HOH
24
A
HOH
25
3
HOH
HOH
25
A
HOH
26
3
HOH
HOH
26
A
HOH
27
3
HOH
HOH
27
A
HOH
28
3
HOH
HOH
28
A
HOH
29
3
HOH
HOH
29
A
HOH
30
3
HOH
HOH
30
A
HOH
31
3
HOH
HOH
31
A
HOH
32
3
HOH
HOH
32
A
HOH
33
3
HOH
HOH
33
A
HOH
34
3
HOH
HOH
34
A
HOH
35
3
HOH
HOH
35
A
HOH
36
3
HOH
HOH
36
A
HOH
37
3
HOH
HOH
37
A
HOH
38
3
HOH
HOH
38
A
HOH
39
3
HOH
HOH
39
A
HOH
40
3
HOH
HOH
40
A
HOH
41
3
HOH
HOH
41
A
HOH
42
3
HOH
HOH
42
A
HOH
43
3
HOH
HOH
43
A
HOH
44
3
HOH
HOH
44
A
HOH
45
3
HOH
HOH
45
A
HOH
46
3
HOH
HOH
46
A
HOH
47
3
HOH
HOH
47
A
HOH
48
3
HOH
HOH
48
A
HOH
49
3
HOH
HOH
49
A
HOH
50
3
HOH
HOH
50
A
HOH
51
3
HOH
HOH
51
A
HOH
52
3
HOH
HOH
52
A
HOH
53
3
HOH
HOH
53
A
HOH
54
3
HOH
HOH
54
A
HOH
55
3
HOH
HOH
55
A
HOH
56
3
HOH
HOH
56
A
HOH
57
3
HOH
HOH
57
A
HOH
58
3
HOH
HOH
58
A
HOH
59
3
HOH
HOH
59
A
HOH
60
3
HOH
HOH
60
A
HOH
61
3
HOH
HOH
61
A
HOH
62
3
HOH
HOH
62
A
HOH
63
3
HOH
HOH
63
A
HOH
64
3
HOH
HOH
64
A
HOH
65
3
HOH
HOH
65
A
HOH
66
3
HOH
HOH
66
A
HOH
67
3
HOH
HOH
67
A
HOH
68
3
HOH
HOH
68
A
HOH
69
3
HOH
HOH
69
A
HOH
1
3
HOH
HOH
226
A
HOH
2
3
HOH
HOH
227
A
HOH
3
3
HOH
HOH
228
A
HOH
4
3
HOH
HOH
229
A
HOH
5
3
HOH
HOH
230
A
HOH
6
3
HOH
HOH
231
A
HOH
7
3
HOH
HOH
232
A
HOH
8
3
HOH
HOH
233
A
HOH
9
3
HOH
HOH
234
A
HOH
10
3
HOH
HOH
235
A
HOH
11
3
HOH
HOH
236
A
HOH
12
3
HOH
HOH
237
A
HOH
13
3
HOH
HOH
238
A
n
1
133
A
n
2
134
A
n
3
135
A
SER
136
n
4
SER
136
A
VAL
137
n
5
VAL
137
A
LYS
138
n
6
LYS
138
A
ILE
139
n
7
ILE
139
A
ILE
140
n
8
ILE
140
A
ARG
141
n
9
ARG
141
A
LEU
142
n
10
LEU
142
A
VAL
143
n
11
VAL
143
A
LYS
144
n
12
LYS
144
A
ASN
145
n
13
ASN
145
A
ARG
146
n
14
ARG
146
A
GLU
147
n
15
GLU
147
A
PRO
148
n
16
PRO
148
A
LEU
149
n
17
LEU
149
A
GLY
150
n
18
GLY
150
A
ALA
151
n
19
ALA
151
A
THR
152
n
20
THR
152
A
ILE
153
n
21
ILE
153
A
LYS
154
n
22
LYS
154
A
LYS
155
n
23
LYS
155
A
ASP
156
n
24
ASP
156
A
GLU
157
n
25
GLU
157
A
GLN
158
n
26
GLN
158
A
THR
159
n
27
THR
159
A
GLY
160
n
28
GLY
160
A
ALA
161
n
29
ALA
161
A
ILE
162
n
30
ILE
162
A
ILE
163
n
31
ILE
163
A
VAL
164
n
32
VAL
164
A
ALA
165
n
33
ALA
165
A
ARG
166
n
34
ARG
166
A
ILE
167
n
35
ILE
167
A
MSE
168
n
36
MSE
168
A
ARG
169
n
37
ARG
169
A
GLY
170
n
38
GLY
170
A
GLY
171
n
39
GLY
171
A
ALA
172
n
40
ALA
172
A
ALA
173
n
41
ALA
173
A
ASP
174
n
42
ASP
174
A
ARG
175
n
43
ARG
175
A
SER
176
n
44
SER
176
A
GLY
177
n
45
GLY
177
A
LEU
178
n
46
LEU
178
A
ILE
179
n
47
ILE
179
A
HIS
180
n
48
HIS
180
A
VAL
181
n
49
VAL
181
A
GLY
182
n
50
GLY
182
A
ASP
183
n
51
ASP
183
A
GLU
184
n
52
GLU
184
A
LEU
185
n
53
LEU
185
A
ARG
186
n
54
ARG
186
A
GLU
187
n
55
GLU
187
A
VAL
188
n
56
VAL
188
A
ASN
189
n
57
ASN
189
A
GLY
190
n
58
GLY
190
A
ILE
191
n
59
ILE
191
A
PRO
192
n
60
PRO
192
A
VAL
193
n
61
VAL
193
A
GLU
194
n
62
GLU
194
A
ASP
195
n
63
ASP
195
A
LYS
196
n
64
LYS
196
A
ARG
197
n
65
ARG
197
A
PRO
198
n
66
PRO
198
A
GLU
199
n
67
GLU
199
A
GLU
200
n
68
GLU
200
A
ILE
201
n
69
ILE
201
A
ILE
202
n
70
ILE
202
A
GLN
203
n
71
GLN
203
A
ILE
204
n
72
ILE
204
A
LEU
205
n
73
LEU
205
A
ALA
206
n
74
ALA
206
A
GLN
207
n
75
GLN
207
A
SER
208
n
76
SER
208
A
GLN
209
n
77
GLN
209
A
GLY
210
n
78
GLY
210
A
ALA
211
n
79
ALA
211
A
ILE
212
n
80
ILE
212
A
THR
213
n
81
THR
213
A
PHE
214
n
82
PHE
214
A
LYS
215
n
83
LYS
215
A
ILE
216
n
84
ILE
216
A
ILE
217
n
85
ILE
217
A
PRO
218
n
86
PRO
218
A
GLY
219
n
87
GLY
219
A
n
88
220
A
n
89
221
A
n
90
222
A
n
91
223
A
n
92
224
A
n
93
225
A
software_defined_assembly
PISA
3
trimeric
4210
-16
11230
A
MSE
168
SELENOMETHIONINE
A
MSE
36
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_665
-y+1,x-y+1,z
crystal symmetry operation
33.3080000000
57.6911482985
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_565
-x+y,-x+1,z
crystal symmetry operation
-33.3080000000
57.6911482985
0.0000000000
A
N
LEU
142
A
N
LEU
10
A
O
ILE
212
A
O
ILE
80
A
O
LYS
215
A
O
LYS
83
A
N
ARG
186
A
N
ARG
54
A
O
LEU
185
A
O
LEU
53
A
N
ILE
162
A
N
ILE
30
A
O
ALA
165
A
O
ALA
33
A
N
THR
152
A
N
THR
20
A
N
LEU
142
A
N
LEU
10
A
O
ILE
212
A
O
ILE
80
A
O
LYS
215
A
O
LYS
83
A
N
ARG
186
A
N
ARG
54
A
N
VAL
188
A
N
VAL
56
A
O
ILE
191
A
O
ILE
59
1
A
HOH
33
O
HOH
1
A
HOH
49
O
HOH
1
A
CE
LYS
138
A
CE
LYS
6
1
Y
1
A
NZ
LYS
138
A
NZ
LYS
6
1
Y
1
A
NE
ARG
146
A
NE
ARG
14
1
Y
1
A
CZ
ARG
146
A
CZ
ARG
14
1
Y
1
A
NH1
ARG
146
A
NH1
ARG
14
1
Y
1
A
NH2
ARG
146
A
NH2
ARG
14
1
Y
1
A
NZ
LYS
154
A
NZ
LYS
22
1
Y
1
A
CD
GLU
157
A
CD
GLU
25
1
Y
1
A
OE1
GLU
157
A
OE1
GLU
25
1
Y
1
A
OE2
GLU
157
A
OE2
GLU
25
1
Y
1
A
CG
ARG
169
A
CG
ARG
37
1
Y
1
A
CD
ARG
169
A
CD
ARG
37
1
Y
1
A
NE
ARG
169
A
NE
ARG
37
1
Y
1
A
CZ
ARG
169
A
CZ
ARG
37
1
Y
1
A
NH1
ARG
169
A
NH1
ARG
37
1
Y
1
A
NH2
ARG
169
A
NH2
ARG
37
1
Y
1
A
NE
ARG
197
A
NE
ARG
65
1
Y
1
A
CZ
ARG
197
A
CZ
ARG
65
1
Y
1
A
NH1
ARG
197
A
NH1
ARG
65
1
Y
1
A
NH2
ARG
197
A
NH2
ARG
65
1
Y
1
A
CE
LYS
215
A
CE
LYS
83
1
Y
1
A
NZ
LYS
215
A
NZ
LYS
83
1
Y
1
A
GLY
133
A
GLY
1
1
Y
1
A
SER
134
A
SER
2
1
Y
1
A
ASP
135
A
ASP
3
1
Y
1
A
SER
220
A
SER
88
1
Y
1
A
LYS
221
A
LYS
89
1
Y
1
A
GLU
222
A
GLU
90
1
Y
1
A
GLU
223
A
GLU
91
1
Y
1
A
THR
224
A
THR
92
1
Y
1
A
PRO
225
A
PRO
93
1
Y
1
A
A
VAL
GLU
193
194
-149.07
44.670
12.9910
9.100
0.5840
0.2920
0.0000
0.5840
0.0000
-0.8760
0.9590
0.9580
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY .
The structure was originally solved using data measured with the same crystal on a copper rotating anode. The model was refined against higher resolution synchrotron data. Scaled synchrotron intensities have been deposited along with the structure factors.
0.1908
0.1839
0.1840
1.3000
33.3080
1449
28929
5.0090
99.8070
0.1950
0.1920
1.000
0.010
1.1950
0.0240
RANDOM
2
THROUGHOUT
0.000
SAD
0.046
0.0420
0.8000
0.8000
1.4000
MAXIMUM LIKELIHOOD
MASK BULK SOLVENT
1.3000
33.3080
69
699
13
0
617
0.018
0.022
700
0.002
0.020
493
1.679
1.987
963
0.921
3.000
1231
6.733
5.000
105
36.165
25.000
26
10.900
15.000
140
6.682
15.000
5
0.110
0.200
119
0.008
0.021
792
0.001
0.020
121
1.902
1.500
453
0.565
1.500
185
2.973
2.000
749
3.989
3.000
247
6.028
4.500
203
1.413
3.000
1193
0.238
0.217
1.334
114
2020
2137
20
99.860
0.221
0.196
1.370
103
1972
2075
20
100.000
0.164
0.169
1.410
131
1877
2012
20
99.801
0.210
0.166
1.453
96
1866
1964
20
99.898
0.165
0.145
1.501
113
1785
1900
20
99.895
0.185
0.152
1.553
84
1745
1832
20
99.836
0.207
0.155
1.612
84
1689
1774
20
99.944
0.151
0.153
1.677
76
1647
1725
20
99.884
0.188
0.158
1.752
75
1565
1641
20
99.939
0.168
0.159
1.837
73
1496
1571
20
99.873
0.206
0.157
1.936
74
1421
1497
20
99.866
0.187
0.155
2.053
60
1337
1399
20
99.857
0.156
0.155
2.194
84
1257
1342
20
99.925
0.122
0.150
2.369
47
1199
1246
20
100.000
0.203
0.187
2.594
55
1093
1151
20
99.739
0.187
0.200
2.898
37
1007
1045
20
99.904
0.192
0.215
3.342
53
856
909
20
100.000
0.199
0.195
4.083
34
752
786
20
100.000
0.206
0.196
5.731
35
581
619
20
99.515
0.310
0.324
33.308
21
315
360
20
93.333
1.300
40.000
3O46
28982
0.041
1.566
2,1
14.600
5.600
99.800
0.751
1.300
1.320
2847
1.660
5.500
100.000
0.663
1.320
1.350
2815
1.599
5.500
99.800
0.522
1.350
1.370
2882
1.610
5.500
99.900
0.421
1.370
1.400
2844
1.514
5.500
100.000
0.369
1.400
1.430
2821
1.491
5.500
99.900
0.320
1.430
1.460
2850
1.453
5.600
99.900
0.231
1.460
1.500
2899
1.410
5.600
99.900
0.189
1.500
1.540
2812
1.430
5.600
100.000
0.159
1.540
1.590
2852
1.419
5.600
100.000
0.128
1.590
1.640
2801
1.389
5.600
100.000
0.101
1.640
1.700
2904
1.441
5.600
100.000
0.084
1.700
1.760
2837
1.409
5.600
100.000
0.068
1.760
1.840
2877
1.459
5.700
100.000
0.054
1.840
1.940
2835
1.587
5.700
100.000
0.053
1.940
2.060
2809
2.031
5.700
100.000
0.049
2.060
2.220
2885
2.329
5.600
100.000
0.040
2.220
2.450
2849
1.918
5.600
100.000
0.030
2.450
2.800
2865
1.429
5.500
100.000
0.027
2.800
3.530
2837
1.419
5.800
100.000
0.025
3.530
40.000
2800
1.308
5.500
97.700
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
phasing
George M. Sheldrick
gsheldr@shelx.uni-ac.gwdg.de
Fortran_77
http://shelx.uni-ac.gwdg.de/SHELX/
SHELX
package
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
5.5.0109
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
phasing
SHELXDE
N
MAGUK p55 subfamily member 7
Crystal structure of the PDZ domain of MPP7
1
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
2
N
N
3
N
N
A
GLY
171
A
GLY
39
HELX_P
A
GLY
177
A
GLY
45
1
1
7
A
ARG
197
A
ARG
65
HELX_P
A
SER
208
A
SER
76
1
2
12
covale
1.315
A
ILE
167
A
C
ILE
35
1_555
A
MSE
168
A
N
MSE
36
1_555
covale
1.342
A
MSE
168
A
C
MSE
36
1_555
A
ARG
169
A
N
ARG
37
1_555
PROTEIN BINDING
pdz domain, structural genomics consortium, SGC, PROTEIN BINDING
MPP7_HUMAN
UNP
1
135
Q5T2T1
DSVKIIRLVKNREPLGATIKKDEQTGAIIVARIMRGGAADRSGLIHVGDELREVNGIPVEDKRPEEIIQILAQSQGAITF
KIIPGSKEETP
135
225
3O46
135
225
Q5T2T1
A
1
3
93
1
EXPRESSION TAG
GLY
133
3O46
A
Q5T2T1
UNP
1
1
EXPRESSION TAG
SER
134
3O46
A
Q5T2T1
UNP
2
5
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
138
A
LYS
6
A
LYS
144
A
LYS
12
A
GLY
210
A
GLY
78
A
ILE
217
A
ILE
85
A
GLU
184
A
GLU
52
A
VAL
188
A
VAL
56
A
ILE
162
A
ILE
30
A
ILE
167
A
ILE
35
A
ALA
151
A
ALA
19
A
LYS
155
A
LYS
23
A
LYS
138
A
LYS
6
A
LYS
144
A
LYS
12
A
GLY
210
A
GLY
78
A
ILE
217
A
ILE
85
A
GLU
184
A
GLU
52
A
VAL
188
A
VAL
56
A
ILE
191
A
ILE
59
A
PRO
192
A
PRO
60
173
P 63