0.026717
0.000000
0.000000
-0.000000
0.020236
0.000000
0.000000
-0.000000
0.012062
0.000000
0.000000
0.000000
Joint Center for Structural Genomics (JCSG)
Shapiro, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
37.429
49.416
82.905
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 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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
To be published
0353
Crystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)
10.2210/pdb4yme/pdb
pdb_00004yme
100
1
Vertical focusing mirror; double crystal Si(111) monochromator
CCD
2014-12-06
MARMOSAIC 325 mm CCD
double crystal Si(111)
SINGLE WAVELENGTH
M
x-ray
1
0.97952
1.0
BL14-1
SSRL
0.97952
SYNCHROTRON
SSRL BEAMLINE BL14-1
16774.033
sensory box/GGDEF family protein
UNP residues 372-528
1
man
polymer
18.015
water
186
nat
water
no
yes
GAEHDGLTGLLNRNSLQ(MSE)RLAAAIDRVEASGESLAVICIDLDHFKEANDQHGHLAGDALLVETARRLQSAVQAPSF
AARLGGDEFIVVQIAGGDQPAVAAELAGRLIE(MSE)LAAPVPFDGQELA(MSE)GSSLGVSLYPDDGRTAEAL(MSE)A
NAD(MSE)ALYRAKESGR
GAEHDGLTGLLNRNSLQMRLAAAIDRVEASGESLAVICIDLDHFKEANDQHGHLAGDALLVETARRLQSAVQAPSFAARL
GGDEFIVVQIAGGDQPAVAAELAGRLIEMLAAPVPFDGQELAMGSSLGVSLYPDDGRTAEALMANADMALYRAKESGR
A
JCSG-430430
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
ATCC 19089 / CB15
sample
1
158
CC_0091
190650
Caulobacter crescentus
562
Escherichia Coli
PB1
Plasmid
Biological sequence
SpeedET
1
2.11
41.67
VAPOR DIFFUSION, SITTING DROP
0.2M magnesium formate, 20% polyethylene glycol 3350
277
Joint Center for Structural Genomics
JCSG
PSI:Biology
entity_src_gen
pdbx_struct_assembly
pdbx_struct_oper_list
software
citation_author
database_2
struct_ref_seq_dif
repository
Initial release
Derived calculations
Refinement description
Source and taxonomy
Database references
Database references
1
0
2015-04-01
1
1
2017-11-22
1
2
2018-01-24
1
3
2023-02-01
_entity_src_gen.pdbx_alt_source_flag
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_oper_list.symmetry_operation
_software.classification
_citation_author.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2015-03-06
REL
REL
1
A
O
HOH
786
6.78
HOH
water
THE CONSTRUCT (372-528) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
HOH
939
2
HOH
HOH
601
A
HOH
1068
2
HOH
HOH
602
A
HOH
1074
2
HOH
HOH
603
A
HOH
969
2
HOH
HOH
604
A
HOH
993
2
HOH
HOH
605
A
HOH
978
2
HOH
HOH
606
A
HOH
951
2
HOH
HOH
607
A
HOH
1000
2
HOH
HOH
608
A
HOH
1071
2
HOH
HOH
609
A
HOH
1022
2
HOH
HOH
610
A
HOH
1019
2
HOH
HOH
611
A
HOH
976
2
HOH
HOH
612
A
HOH
1032
2
HOH
HOH
613
A
HOH
933
2
HOH
HOH
614
A
HOH
1028
2
HOH
HOH
615
A
HOH
1046
2
HOH
HOH
616
A
HOH
1033
2
HOH
HOH
617
A
HOH
1026
2
HOH
HOH
618
A
HOH
1086
2
HOH
HOH
619
A
HOH
961
2
HOH
HOH
620
A
HOH
1006
2
HOH
HOH
621
A
HOH
921
2
HOH
HOH
622
A
HOH
914
2
HOH
HOH
623
A
HOH
991
2
HOH
HOH
624
A
HOH
918
2
HOH
HOH
625
A
HOH
952
2
HOH
HOH
626
A
HOH
1029
2
HOH
HOH
627
A
HOH
1031
2
HOH
HOH
628
A
HOH
924
2
HOH
HOH
629
A
HOH
937
2
HOH
HOH
630
A
HOH
916
2
HOH
HOH
631
A
HOH
1037
2
HOH
HOH
632
A
HOH
1070
2
HOH
HOH
633
A
HOH
1052
2
HOH
HOH
634
A
HOH
965
2
HOH
HOH
635
A
HOH
1027
2
HOH
HOH
636
A
HOH
1020
2
HOH
HOH
637
A
HOH
1018
2
HOH
HOH
638
A
HOH
946
2
HOH
HOH
639
A
HOH
1001
2
HOH
HOH
640
A
HOH
1054
2
HOH
HOH
641
A
HOH
979
2
HOH
HOH
642
A
HOH
1057
2
HOH
HOH
643
A
HOH
926
2
HOH
HOH
644
A
HOH
941
2
HOH
HOH
645
A
HOH
908
2
HOH
HOH
646
A
HOH
1045
2
HOH
HOH
647
A
HOH
997
2
HOH
HOH
648
A
HOH
1007
2
HOH
HOH
649
A
HOH
1030
2
HOH
HOH
650
A
HOH
1023
2
HOH
HOH
651
A
HOH
943
2
HOH
HOH
652
A
HOH
928
2
HOH
HOH
653
A
HOH
911
2
HOH
HOH
654
A
HOH
919
2
HOH
HOH
655
A
HOH
1012
2
HOH
HOH
656
A
HOH
907
2
HOH
HOH
657
A
HOH
1038
2
HOH
HOH
658
A
HOH
989
2
HOH
HOH
659
A
HOH
1041
2
HOH
HOH
660
A
HOH
930
2
HOH
HOH
661
A
HOH
942
2
HOH
HOH
662
A
HOH
1035
2
HOH
HOH
663
A
HOH
903
2
HOH
HOH
664
A
HOH
950
2
HOH
HOH
665
A
HOH
967
2
HOH
HOH
666
A
HOH
910
2
HOH
HOH
667
A
HOH
1058
2
HOH
HOH
668
A
HOH
938
2
HOH
HOH
669
A
HOH
953
2
HOH
HOH
670
A
HOH
1034
2
HOH
HOH
671
A
HOH
984
2
HOH
HOH
672
A
HOH
1021
2
HOH
HOH
673
A
HOH
1051
2
HOH
HOH
674
A
HOH
915
2
HOH
HOH
675
A
HOH
906
2
HOH
HOH
676
A
HOH
986
2
HOH
HOH
677
A
HOH
949
2
HOH
HOH
678
A
HOH
1040
2
HOH
HOH
679
A
HOH
901
2
HOH
HOH
680
A
HOH
931
2
HOH
HOH
681
A
HOH
966
2
HOH
HOH
682
A
HOH
905
2
HOH
HOH
683
A
HOH
963
2
HOH
HOH
684
A
HOH
1044
2
HOH
HOH
685
A
HOH
904
2
HOH
HOH
686
A
HOH
902
2
HOH
HOH
687
A
HOH
1072
2
HOH
HOH
688
A
HOH
923
2
HOH
HOH
689
A
HOH
1024
2
HOH
HOH
690
A
HOH
917
2
HOH
HOH
691
A
HOH
936
2
HOH
HOH
692
A
HOH
981
2
HOH
HOH
693
A
HOH
929
2
HOH
HOH
694
A
HOH
1017
2
HOH
HOH
695
A
HOH
1010
2
HOH
HOH
696
A
HOH
1015
2
HOH
HOH
697
A
HOH
934
2
HOH
HOH
698
A
HOH
1055
2
HOH
HOH
699
A
HOH
968
2
HOH
HOH
700
A
HOH
970
2
HOH
HOH
701
A
HOH
1053
2
HOH
HOH
702
A
HOH
944
2
HOH
HOH
703
A
HOH
1042
2
HOH
HOH
704
A
HOH
974
2
HOH
HOH
705
A
HOH
980
2
HOH
HOH
706
A
HOH
973
2
HOH
HOH
707
A
HOH
912
2
HOH
HOH
708
A
HOH
909
2
HOH
HOH
709
A
HOH
971
2
HOH
HOH
710
A
HOH
925
2
HOH
HOH
711
A
HOH
948
2
HOH
HOH
712
A
HOH
998
2
HOH
HOH
713
A
HOH
927
2
HOH
HOH
714
A
HOH
1003
2
HOH
HOH
715
A
HOH
977
2
HOH
HOH
716
A
HOH
932
2
HOH
HOH
717
A
HOH
1016
2
HOH
HOH
718
A
HOH
1009
2
HOH
HOH
719
A
HOH
1059
2
HOH
HOH
720
A
HOH
922
2
HOH
HOH
721
A
HOH
1025
2
HOH
HOH
722
A
HOH
920
2
HOH
HOH
723
A
HOH
945
2
HOH
HOH
724
A
HOH
940
2
HOH
HOH
725
A
HOH
1005
2
HOH
HOH
726
A
HOH
1039
2
HOH
HOH
727
A
HOH
1065
2
HOH
HOH
728
A
HOH
990
2
HOH
HOH
729
A
HOH
935
2
HOH
HOH
730
A
HOH
1036
2
HOH
HOH
731
A
HOH
1056
2
HOH
HOH
732
A
HOH
1043
2
HOH
HOH
733
A
HOH
975
2
HOH
HOH
734
A
HOH
1083
2
HOH
HOH
735
A
HOH
1069
2
HOH
HOH
736
A
HOH
1060
2
HOH
HOH
737
A
HOH
982
2
HOH
HOH
738
A
HOH
1011
2
HOH
HOH
739
A
HOH
1048
2
HOH
HOH
740
A
HOH
1014
2
HOH
HOH
741
A
HOH
1066
2
HOH
HOH
742
A
HOH
1047
2
HOH
HOH
743
A
HOH
1079
2
HOH
HOH
744
A
HOH
1082
2
HOH
HOH
745
A
HOH
987
2
HOH
HOH
746
A
HOH
1084
2
HOH
HOH
747
A
HOH
913
2
HOH
HOH
748
A
HOH
947
2
HOH
HOH
749
A
HOH
1085
2
HOH
HOH
750
A
HOH
992
2
HOH
HOH
751
A
HOH
983
2
HOH
HOH
752
A
HOH
1049
2
HOH
HOH
753
A
HOH
994
2
HOH
HOH
754
A
HOH
972
2
HOH
HOH
755
A
HOH
1081
2
HOH
HOH
756
A
HOH
1080
2
HOH
HOH
757
A
HOH
1004
2
HOH
HOH
758
A
HOH
1002
2
HOH
HOH
759
A
HOH
988
2
HOH
HOH
760
A
HOH
1078
2
HOH
HOH
761
A
HOH
1064
2
HOH
HOH
762
A
HOH
1077
2
HOH
HOH
763
A
HOH
962
2
HOH
HOH
764
A
HOH
1050
2
HOH
HOH
765
A
HOH
1062
2
HOH
HOH
766
A
HOH
1063
2
HOH
HOH
767
A
HOH
995
2
HOH
HOH
768
A
HOH
956
2
HOH
HOH
769
A
HOH
955
2
HOH
HOH
770
A
HOH
985
2
HOH
HOH
771
A
HOH
999
2
HOH
HOH
772
A
HOH
960
2
HOH
HOH
773
A
HOH
996
2
HOH
HOH
774
A
HOH
1061
2
HOH
HOH
775
A
HOH
964
2
HOH
HOH
776
A
HOH
1008
2
HOH
HOH
777
A
HOH
959
2
HOH
HOH
778
A
HOH
1076
2
HOH
HOH
779
A
HOH
958
2
HOH
HOH
780
A
HOH
954
2
HOH
HOH
781
A
HOH
957
2
HOH
HOH
782
A
HOH
1075
2
HOH
HOH
783
A
HOH
1073
2
HOH
HOH
784
A
HOH
1013
2
HOH
HOH
785
A
HOH
1067
2
HOH
HOH
786
A
n
1
371
A
ALA
372
n
2
ALA
372
A
GLU
373
n
3
GLU
373
A
HIS
374
n
4
HIS
374
A
ASP
375
n
5
ASP
375
A
GLY
376
n
6
GLY
376
A
LEU
377
n
7
LEU
377
A
THR
378
n
8
THR
378
A
GLY
379
n
9
GLY
379
A
LEU
380
n
10
LEU
380
A
LEU
381
n
11
LEU
381
A
ASN
382
n
12
ASN
382
A
ARG
383
n
13
ARG
383
A
ASN
384
n
14
ASN
384
A
SER
385
n
15
SER
385
A
LEU
386
n
16
LEU
386
A
GLN
387
n
17
GLN
387
A
MSE
388
n
18
MSE
388
A
ARG
389
n
19
ARG
389
A
LEU
390
n
20
LEU
390
A
ALA
391
n
21
ALA
391
A
ALA
392
n
22
ALA
392
A
ALA
393
n
23
ALA
393
A
ILE
394
n
24
ILE
394
A
ASP
395
n
25
ASP
395
A
ARG
396
n
26
ARG
396
A
VAL
397
n
27
VAL
397
A
GLU
398
n
28
GLU
398
A
ALA
399
n
29
ALA
399
A
SER
400
n
30
SER
400
A
GLY
401
n
31
GLY
401
A
GLU
402
n
32
GLU
402
A
SER
403
n
33
SER
403
A
LEU
404
n
34
LEU
404
A
ALA
405
n
35
ALA
405
A
VAL
406
n
36
VAL
406
A
ILE
407
n
37
ILE
407
A
CYS
408
n
38
CYS
408
A
ILE
409
n
39
ILE
409
A
ASP
410
n
40
ASP
410
A
LEU
411
n
41
LEU
411
A
ASP
412
n
42
ASP
412
A
HIS
413
n
43
HIS
413
A
PHE
414
n
44
PHE
414
A
LYS
415
n
45
LYS
415
A
GLU
416
n
46
GLU
416
A
ALA
417
n
47
ALA
417
A
ASN
418
n
48
ASN
418
A
ASP
419
n
49
ASP
419
A
GLN
420
n
50
GLN
420
A
HIS
421
n
51
HIS
421
A
GLY
422
n
52
GLY
422
A
HIS
423
n
53
HIS
423
A
LEU
424
n
54
LEU
424
A
ALA
425
n
55
ALA
425
A
GLY
426
n
56
GLY
426
A
ASP
427
n
57
ASP
427
A
ALA
428
n
58
ALA
428
A
LEU
429
n
59
LEU
429
A
LEU
430
n
60
LEU
430
A
VAL
431
n
61
VAL
431
A
GLU
432
n
62
GLU
432
A
THR
433
n
63
THR
433
A
ALA
434
n
64
ALA
434
A
ARG
435
n
65
ARG
435
A
ARG
436
n
66
ARG
436
A
LEU
437
n
67
LEU
437
A
GLN
438
n
68
GLN
438
A
SER
439
n
69
SER
439
A
ALA
440
n
70
ALA
440
A
VAL
441
n
71
VAL
441
A
GLN
442
n
72
GLN
442
A
ALA
443
n
73
ALA
443
A
PRO
444
n
74
PRO
444
A
SER
445
n
75
SER
445
A
PHE
446
n
76
PHE
446
A
ALA
447
n
77
ALA
447
A
ALA
448
n
78
ALA
448
A
ARG
449
n
79
ARG
449
A
LEU
450
n
80
LEU
450
A
GLY
451
n
81
GLY
451
A
GLY
452
n
82
GLY
452
A
ASP
453
n
83
ASP
453
A
GLU
454
n
84
GLU
454
A
PHE
455
n
85
PHE
455
A
ILE
456
n
86
ILE
456
A
VAL
457
n
87
VAL
457
A
VAL
458
n
88
VAL
458
A
GLN
459
n
89
GLN
459
A
ILE
460
n
90
ILE
460
A
ALA
461
n
91
ALA
461
A
GLY
462
n
92
GLY
462
A
GLY
463
n
93
GLY
463
A
ASP
464
n
94
ASP
464
A
GLN
465
n
95
GLN
465
A
PRO
466
n
96
PRO
466
A
ALA
467
n
97
ALA
467
A
VAL
468
n
98
VAL
468
A
ALA
469
n
99
ALA
469
A
ALA
470
n
100
ALA
470
A
GLU
471
n
101
GLU
471
A
LEU
472
n
102
LEU
472
A
ALA
473
n
103
ALA
473
A
GLY
474
n
104
GLY
474
A
ARG
475
n
105
ARG
475
A
LEU
476
n
106
LEU
476
A
ILE
477
n
107
ILE
477
A
GLU
478
n
108
GLU
478
A
MSE
479
n
109
MSE
479
A
LEU
480
n
110
LEU
480
A
ALA
481
n
111
ALA
481
A
ALA
482
n
112
ALA
482
A
PRO
483
n
113
PRO
483
A
VAL
484
n
114
VAL
484
A
PRO
485
n
115
PRO
485
A
PHE
486
n
116
PHE
486
A
ASP
487
n
117
ASP
487
A
GLY
488
n
118
GLY
488
A
GLN
489
n
119
GLN
489
A
GLU
490
n
120
GLU
490
A
LEU
491
n
121
LEU
491
A
ALA
492
n
122
ALA
492
A
MSE
493
n
123
MSE
493
A
GLY
494
n
124
GLY
494
A
SER
495
n
125
SER
495
A
SER
496
n
126
SER
496
A
LEU
497
n
127
LEU
497
A
GLY
498
n
128
GLY
498
A
VAL
499
n
129
VAL
499
A
SER
500
n
130
SER
500
A
LEU
501
n
131
LEU
501
A
TYR
502
n
132
TYR
502
A
PRO
503
n
133
PRO
503
A
ASP
504
n
134
ASP
504
A
ASP
505
n
135
ASP
505
A
GLY
506
n
136
GLY
506
A
ARG
507
n
137
ARG
507
A
THR
508
n
138
THR
508
A
ALA
509
n
139
ALA
509
A
GLU
510
n
140
GLU
510
A
ALA
511
n
141
ALA
511
A
LEU
512
n
142
LEU
512
A
MSE
513
n
143
MSE
513
A
ALA
514
n
144
ALA
514
A
ASN
515
n
145
ASN
515
A
ALA
516
n
146
ALA
516
A
ASP
517
n
147
ASP
517
A
MSE
518
n
148
MSE
518
A
ALA
519
n
149
ALA
519
A
LEU
520
n
150
LEU
520
A
TYR
521
n
151
TYR
521
A
ARG
522
n
152
ARG
522
A
ALA
523
n
153
ALA
523
A
LYS
524
n
154
LYS
524
A
GLU
525
n
155
GLU
525
A
SER
526
n
156
SER
526
A
GLY
527
n
157
GLY
527
A
n
158
528
A
0.2404
-0.2939
0.0214
0.7286
0.1570
0.4256
-0.0191
0.0128
-0.0133
-0.0159
-0.0102
-0.0034
-0.0078
0.0223
0.0293
0.0114
-0.0028
0.0108
0.0073
-0.0016
0.0138
refined
21.9336
17.3673
9.2369
X-RAY DIFFRACTION
A
372
A
527
X-RAY DIFFRACTION
1
author_and_software_defined_assembly
PISA
1
monomeric
A
MSE
388
modified residue
A
MSE
18
MET
A
MSE
479
modified residue
A
MSE
109
MET
A
MSE
493
modified residue
A
MSE
123
MET
A
MSE
513
modified residue
A
MSE
143
MET
A
MSE
518
modified residue
A
MSE
148
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
A
N
PHE
446
A
N
PHE
76
A
O
VAL
458
A
O
VAL
88
A
O
PHE
455
A
O
PHE
85
A
N
ILE
409
A
N
ILE
39
A
N
VAL
406
A
N
VAL
36
A
O
SER
500
A
O
SER
130
A
N
PHE
486
A
N
PHE
116
A
O
GLN
489
A
O
GLN
119
1
A
GLY
371
A
GLY
1
1
Y
1
A
ARG
528
A
ARG
158
1
Y
1
3.55
0.50
120.30
123.85
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
449
449
449
N
1
A
MSE
493
-103.50
-145.64
1
A
MSE
493
-97.50
-148.68
74.790
26.8077
13.570
2.2700
0.0000
-0.0000
-1.5500
0.0000
-0.7300
0.9690
0.9560
1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT
0.2048
0.1827
0.1839
1.4000
23.679
1546
29187
30733
5.0000
99.0000
1.000
0.230
2.9390
0.0540
RANDOM
1
THROUGHOUT
0.000
SAD
0.0640
0.0640
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD WITH PHASES
MASK
1.4000
23.679
186
1328
0
0
1142
0.020
0.022
1256
0.002
0.020
1215
1.785
1.969
1720
1.015
3.000
2806
5.883
5.000
186
35.803
24.839
62
12.982
15.000
217
15.752
15.000
11
0.113
0.200
196
0.008
0.020
1509
0.001
0.020
282
1.673
2.091
655
1.665
2.086
654
2.735
3.130
825
0.3780
0.3560
1.4360
117
2045
2162
20
95.8300
19.725
0.999
1.40
23.679
4YME
30788
-3.000
0.030
0.038
1
15.620
145154
6.17
98.300
0.563
0.946
1.400
1.450
1.4
14061
5849
5650
1.187
1
96.600
0.794
0.568
1.450
1.510
2.3
14933
6049
6007
0.716
99.300
0.921
0.338
1.510
1.580
3.7
14614
5883
5858
0.425
99.600
0.959
0.223
1.580
1.660
5.3
14096
5635
5612
0.280
99.600
0.978
0.155
1.660
1.760
7.4
14190
5660
5625
0.194
99.400
0.993
0.087
1.760
1.900
11.6
15090
6028
5971
0.110
99.100
0.997
0.048
1.900
2.090
18.8
14503
5819
5729
0.060
98.500
0.998
0.030
2.090
2.390
27.9
14742
5863
5785
0.039
98.700
0.999
0.022
2.390
3.010
35.4
14676
5858
5743
0.028
98.000
0.999
0.018
3.010
43.5
14249
5931
5581
0.023
94.100
data extraction
PDB_EXTRACT
3.10
phasing
SHELX
phasing
SHARP
data scaling
XDS
November 3, 2014 BUILT=20141118
refinement
REFMAC
5.8.0103
data scaling
XSCALE
phasing
SHELXD
Crystal structure of a sensory box/GGDEF family protein (CC_0091) from Caulobacter crescentus CB15 at 1.40 A resolution (PSI Community Target, Shapiro)
1
N
N
2
N
N
A
ASN
382
A
ASN
12
HELX_P
A
GLY
401
A
GLY
31
1
AA1
20
A
HIS
413
A
HIS
43
HELX_P
A
GLY
422
A
GLY
52
1
AA2
10
A
GLY
422
A
GLY
52
HELX_P
A
VAL
441
A
VAL
71
1
AA3
20
A
ASP
464
A
ASP
94
HELX_P
A
LEU
480
A
LEU
110
1
AA4
17
A
THR
508
A
THR
138
HELX_P
A
GLY
527
A
GLY
157
1
AA5
20
covale
1.340
both
A
GLN
387
A
C
GLN
17
1_555
A
MSE
388
A
N
MSE
18
1_555
covale
1.313
both
A
MSE
388
A
C
MSE
18
1_555
A
ARG
389
A
N
ARG
19
1_555
covale
1.319
both
A
GLU
478
A
C
GLU
108
1_555
A
MSE
479
A
N
MSE
109
1_555
covale
1.326
both
A
MSE
479
A
C
MSE
109
1_555
A
LEU
480
A
N
LEU
110
1_555
covale
1.331
both
A
ALA
492
A
C
ALA
122
1_555
A
MSE
493
A
N
MSE
123
1_555
covale
1.331
both
A
MSE
493
A
C
MSE
123
1_555
A
GLY
494
A
N
GLY
124
1_555
covale
1.325
both
A
LEU
512
A
C
LEU
142
1_555
A
MSE
513
A
N
MSE
143
1_555
covale
1.336
both
A
MSE
513
A
C
MSE
143
1_555
A
ALA
514
A
N
ALA
144
1_555
covale
1.327
both
A
ASP
517
A
C
ASP
147
1_555
A
MSE
518
A
N
MSE
148
1_555
covale
1.328
both
A
MSE
518
A
C
MSE
148
1_555
A
ALA
519
A
N
ALA
149
1_555
LYASE
GGDEF domain, PF00990 family, ferredoxin-like fold, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, LYASE
A
ALA
443
A
ALA
73
1
A
PRO
444
A
PRO
74
17.13
A
TYR
502
A
TYR
132
1
A
PRO
503
A
PRO
133
-0.79
Y091_CAUCR
UNP
1
372
Q9ABX9
AEHDGLTGLLNRNSLQMRLAAAIDRVEASGESLAVICIDLDHFKEANDQHGHLAGDALLVETARRLQSAVQAPSFAARLG
GDEFIVVQIAGGDQPAVAAELAGRLIEMLAAPVPFDGQELAMGSSLGVSLYPDDGRTAEALMANADMALYRAKESGR
372
528
4YME
372
528
Q9ABX9
A
1
2
158
1
expression tag
GLY
371
4YME
A
Q9ABX9
UNP
1
4
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
PHE
446
A
PHE
76
A
GLY
451
A
GLY
81
A
GLU
454
A
GLU
84
A
ALA
461
A
ALA
91
A
SER
403
A
SER
33
A
LEU
411
A
LEU
41
A
SER
495
A
SER
125
A
LEU
501
A
LEU
131
A
VAL
484
A
VAL
114
A
PHE
486
A
PHE
116
A
GLN
489
A
GLN
119
A
LEU
491
A
LEU
121
19
P 21 21 21