0.009328
0.005385
0.000000
0.000000
0.010771
0.000000
0.000000
0.000000
0.007412
0.00000
0.00000
0.00000
Joint Center for Structural Genomics (JCSG)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
107.209
107.209
134.918
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
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
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
Proteins
PSFGEY
0867
0887-3585
56
619
624
10.1002/prot.20164
15229895
Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution
2004
10.2210/pdb1o59/pdb
pdb_00001o59
100
1
100
1
1
CCD
2003-04-17
ADSC QUANTUM 315
CCD
2003-04-17
ADSC QUANTUM 315
single crystal Si(111) bent monochromator
SINGLE WAVELENGTH
M
x-ray
1
double crystal monochromator
MAD
M
x-ray
1
0.976224
1.0
0.979608
1.0
0.918370
1.0
0.979413
1.0
BL11-1
SSRL
0.976224
SYNCHROTRON
SSRL BEAMLINE BL11-1
BL9-2
SSRL
0.979608, 0.918370, 0.979413
SYNCHROTRON
SSRL BEAMLINE BL9-2
40464.828
Allantoicase
3.5.3.4
1
man
polymer
18.015
water
218
nat
water
Allantoate amidinohydrolase
no
yes
MGSDKIHHHHHH(MSE)KFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHS
GAWYDGWETRRHNE(MSE)EYDWVIIK(MSE)GVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVE
IVEKFECGPSQRHLFVRGNGLTKERFTHIKLK(MSE)YPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSD
QHFGSVDNLLLPGRGHD(MSE)SDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESES
SENTGEGTWVELVGKSKTGPDKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY
MGSDKIHHHHHHMKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHSGAWY
DGWETRRHNEMEYDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQR
HLFVRGNGLTKERFTHIKLKMYPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGH
DMSDGWETKRSRQPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESESSENTGEGTWVELVGKSKTGP
DKEHVYEIRKSIRVSHVKLTIIPDGGVKRIRVWGY
A
355059
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
sample
YIR029W
4932
Saccharomyces cerevisiae
562
Escherichia coli
Plasmid
2
2.87
56.81
VAPOR DIFFUSION,SITTING DROP,NANODROP
30% Ethylene Glycol , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
293
VAPOR DIFFUSION,SITTING DROP,NANODROP
30% Ethylene Glycol, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
293
Joint Center for Structural Genomics
JCSG
PSI, Protein Structure Initiative
pdbx_database_related
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Advisory
Version format compliance
Database references
Database references
Derived calculations
1
0
2003-09-02
1
1
2008-04-26
1
2
2011-07-13
1
3
2017-12-20
1
4
2023-01-25
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
Y
RCSB
Y
RCSB
2003-08-22
REL
REL
HOH
water
HOH
501
2
HOH
HOH
501
A
HOH
502
2
HOH
HOH
502
A
HOH
503
2
HOH
HOH
503
A
HOH
504
2
HOH
HOH
504
A
HOH
505
2
HOH
HOH
505
A
HOH
506
2
HOH
HOH
506
A
HOH
507
2
HOH
HOH
507
A
HOH
508
2
HOH
HOH
508
A
HOH
509
2
HOH
HOH
509
A
HOH
510
2
HOH
HOH
510
A
HOH
511
2
HOH
HOH
511
A
HOH
512
2
HOH
HOH
512
A
HOH
513
2
HOH
HOH
513
A
HOH
514
2
HOH
HOH
514
A
HOH
516
2
HOH
HOH
516
A
HOH
518
2
HOH
HOH
518
A
HOH
520
2
HOH
HOH
520
A
HOH
521
2
HOH
HOH
521
A
HOH
522
2
HOH
HOH
522
A
HOH
523
2
HOH
HOH
523
A
HOH
524
2
HOH
HOH
524
A
HOH
525
2
HOH
HOH
525
A
HOH
526
2
HOH
HOH
526
A
HOH
527
2
HOH
HOH
527
A
HOH
528
2
HOH
HOH
528
A
HOH
529
2
HOH
HOH
529
A
HOH
530
2
HOH
HOH
530
A
HOH
531
2
HOH
HOH
531
A
HOH
532
2
HOH
HOH
532
A
HOH
533
2
HOH
HOH
533
A
HOH
534
2
HOH
HOH
534
A
HOH
535
2
HOH
HOH
535
A
HOH
536
2
HOH
HOH
536
A
HOH
537
2
HOH
HOH
537
A
HOH
538
2
HOH
HOH
538
A
HOH
539
2
HOH
HOH
539
A
HOH
540
2
HOH
HOH
540
A
HOH
541
2
HOH
HOH
541
A
HOH
542
2
HOH
HOH
542
A
HOH
543
2
HOH
HOH
543
A
HOH
544
2
HOH
HOH
544
A
HOH
545
2
HOH
HOH
545
A
HOH
546
2
HOH
HOH
546
A
HOH
547
2
HOH
HOH
547
A
HOH
548
2
HOH
HOH
548
A
HOH
549
2
HOH
HOH
549
A
HOH
550
2
HOH
HOH
550
A
HOH
551
2
HOH
HOH
551
A
HOH
552
2
HOH
HOH
552
A
HOH
553
2
HOH
HOH
553
A
HOH
554
2
HOH
HOH
554
A
HOH
555
2
HOH
HOH
555
A
HOH
556
2
HOH
HOH
556
A
HOH
557
2
HOH
HOH
557
A
HOH
558
2
HOH
HOH
558
A
HOH
559
2
HOH
HOH
559
A
HOH
560
2
HOH
HOH
560
A
HOH
561
2
HOH
HOH
561
A
HOH
562
2
HOH
HOH
562
A
HOH
563
2
HOH
HOH
563
A
HOH
564
2
HOH
HOH
564
A
HOH
565
2
HOH
HOH
565
A
HOH
566
2
HOH
HOH
566
A
HOH
567
2
HOH
HOH
567
A
HOH
568
2
HOH
HOH
568
A
HOH
569
2
HOH
HOH
569
A
HOH
570
2
HOH
HOH
570
A
HOH
571
2
HOH
HOH
571
A
HOH
573
2
HOH
HOH
573
A
HOH
575
2
HOH
HOH
575
A
HOH
576
2
HOH
HOH
576
A
HOH
577
2
HOH
HOH
577
A
HOH
578
2
HOH
HOH
578
A
HOH
579
2
HOH
HOH
579
A
HOH
580
2
HOH
HOH
580
A
HOH
581
2
HOH
HOH
581
A
HOH
582
2
HOH
HOH
582
A
HOH
583
2
HOH
HOH
583
A
HOH
584
2
HOH
HOH
584
A
HOH
585
2
HOH
HOH
585
A
HOH
586
2
HOH
HOH
586
A
HOH
587
2
HOH
HOH
587
A
HOH
588
2
HOH
HOH
588
A
HOH
590
2
HOH
HOH
590
A
HOH
591
2
HOH
HOH
591
A
HOH
592
2
HOH
HOH
592
A
HOH
593
2
HOH
HOH
593
A
HOH
595
2
HOH
HOH
595
A
HOH
596
2
HOH
HOH
596
A
HOH
597
2
HOH
HOH
597
A
HOH
598
2
HOH
HOH
598
A
HOH
599
2
HOH
HOH
599
A
HOH
601
2
HOH
HOH
601
A
HOH
602
2
HOH
HOH
602
A
HOH
603
2
HOH
HOH
603
A
HOH
604
2
HOH
HOH
604
A
HOH
605
2
HOH
HOH
605
A
HOH
606
2
HOH
HOH
606
A
HOH
608
2
HOH
HOH
608
A
HOH
611
2
HOH
HOH
611
A
HOH
613
2
HOH
HOH
613
A
HOH
616
2
HOH
HOH
616
A
HOH
617
2
HOH
HOH
617
A
HOH
618
2
HOH
HOH
618
A
HOH
619
2
HOH
HOH
619
A
HOH
620
2
HOH
HOH
620
A
HOH
621
2
HOH
HOH
621
A
HOH
622
2
HOH
HOH
622
A
HOH
623
2
HOH
HOH
623
A
HOH
624
2
HOH
HOH
624
A
HOH
625
2
HOH
HOH
625
A
HOH
626
2
HOH
HOH
626
A
HOH
627
2
HOH
HOH
627
A
HOH
628
2
HOH
HOH
628
A
HOH
629
2
HOH
HOH
629
A
HOH
630
2
HOH
HOH
630
A
HOH
631
2
HOH
HOH
631
A
HOH
632
2
HOH
HOH
632
A
HOH
633
2
HOH
HOH
633
A
HOH
634
2
HOH
HOH
634
A
HOH
635
2
HOH
HOH
635
A
HOH
636
2
HOH
HOH
636
A
HOH
637
2
HOH
HOH
637
A
HOH
638
2
HOH
HOH
638
A
HOH
640
2
HOH
HOH
640
A
HOH
641
2
HOH
HOH
641
A
HOH
642
2
HOH
HOH
642
A
HOH
643
2
HOH
HOH
643
A
HOH
644
2
HOH
HOH
644
A
HOH
645
2
HOH
HOH
645
A
HOH
646
2
HOH
HOH
646
A
HOH
647
2
HOH
HOH
647
A
HOH
648
2
HOH
HOH
648
A
HOH
649
2
HOH
HOH
649
A
HOH
650
2
HOH
HOH
650
A
HOH
651
2
HOH
HOH
651
A
HOH
652
2
HOH
HOH
652
A
HOH
653
2
HOH
HOH
653
A
HOH
654
2
HOH
HOH
654
A
HOH
656
2
HOH
HOH
656
A
HOH
658
2
HOH
HOH
658
A
HOH
659
2
HOH
HOH
659
A
HOH
660
2
HOH
HOH
660
A
HOH
661
2
HOH
HOH
661
A
HOH
662
2
HOH
HOH
662
A
HOH
663
2
HOH
HOH
663
A
HOH
664
2
HOH
HOH
664
A
HOH
665
2
HOH
HOH
665
A
HOH
666
2
HOH
HOH
666
A
HOH
668
2
HOH
HOH
668
A
HOH
669
2
HOH
HOH
669
A
HOH
670
2
HOH
HOH
670
A
HOH
671
2
HOH
HOH
671
A
HOH
672
2
HOH
HOH
672
A
HOH
673
2
HOH
HOH
673
A
HOH
674
2
HOH
HOH
674
A
HOH
675
2
HOH
HOH
675
A
HOH
676
2
HOH
HOH
676
A
HOH
677
2
HOH
HOH
677
A
HOH
678
2
HOH
HOH
678
A
HOH
679
2
HOH
HOH
679
A
HOH
680
2
HOH
HOH
680
A
HOH
681
2
HOH
HOH
681
A
HOH
682
2
HOH
HOH
682
A
HOH
683
2
HOH
HOH
683
A
HOH
684
2
HOH
HOH
684
A
HOH
685
2
HOH
HOH
685
A
HOH
686
2
HOH
HOH
686
A
HOH
687
2
HOH
HOH
687
A
HOH
688
2
HOH
HOH
688
A
HOH
689
2
HOH
HOH
689
A
HOH
690
2
HOH
HOH
690
A
HOH
691
2
HOH
HOH
691
A
HOH
692
2
HOH
HOH
692
A
HOH
693
2
HOH
HOH
693
A
HOH
694
2
HOH
HOH
694
A
HOH
695
2
HOH
HOH
695
A
HOH
696
2
HOH
HOH
696
A
HOH
697
2
HOH
HOH
697
A
HOH
698
2
HOH
HOH
698
A
HOH
699
2
HOH
HOH
699
A
HOH
700
2
HOH
HOH
700
A
HOH
701
2
HOH
HOH
701
A
HOH
702
2
HOH
HOH
702
A
HOH
703
2
HOH
HOH
703
A
HOH
704
2
HOH
HOH
704
A
HOH
705
2
HOH
HOH
705
A
HOH
706
2
HOH
HOH
706
A
HOH
707
2
HOH
HOH
707
A
HOH
708
2
HOH
HOH
708
A
HOH
709
2
HOH
HOH
709
A
HOH
712
2
HOH
HOH
712
A
HOH
713
2
HOH
HOH
713
A
HOH
714
2
HOH
HOH
714
A
HOH
715
2
HOH
HOH
715
A
HOH
717
2
HOH
HOH
717
A
HOH
718
2
HOH
HOH
718
A
HOH
719
2
HOH
HOH
719
A
HOH
720
2
HOH
HOH
720
A
HOH
721
2
HOH
HOH
721
A
HOH
722
2
HOH
HOH
722
A
HOH
723
2
HOH
HOH
723
A
HOH
724
2
HOH
HOH
724
A
HOH
725
2
HOH
HOH
725
A
HOH
726
2
HOH
HOH
726
A
HOH
727
2
HOH
HOH
727
A
HOH
728
2
HOH
HOH
728
A
HOH
729
2
HOH
HOH
729
A
HOH
730
2
HOH
HOH
730
A
HOH
731
2
HOH
HOH
731
A
HOH
732
2
HOH
HOH
732
A
HOH
733
2
HOH
HOH
733
A
HOH
734
2
HOH
HOH
734
A
HOH
735
2
HOH
HOH
735
A
HOH
736
2
HOH
HOH
736
A
HOH
737
2
HOH
HOH
737
A
HOH
738
2
HOH
HOH
738
A
HOH
739
2
HOH
HOH
739
A
n
1
-11
A
n
2
-10
A
n
3
-9
A
n
4
-8
A
n
5
-7
A
n
6
-6
A
n
7
-5
A
n
8
-4
A
n
9
-3
A
n
10
-2
A
n
11
-1
A
HIS
0
n
12
HIS
0
A
MSE
1
n
13
MSE
1
A
LYS
2
n
14
LYS
2
A
PHE
3
n
15
PHE
3
A
PHE
4
n
16
PHE
4
A
SER
5
n
17
SER
5
A
LEU
6
n
18
LEU
6
A
ALA
7
n
19
ALA
7
A
ASP
8
n
20
ASP
8
A
GLU
9
n
21
GLU
9
A
ALA
10
n
22
ALA
10
A
GLU
11
n
23
GLU
11
A
PHE
12
n
24
PHE
12
A
LYS
13
n
25
LYS
13
A
SER
14
n
26
SER
14
A
ILE
15
n
27
ILE
15
A
ILE
16
n
28
ILE
16
A
ILE
17
n
29
ILE
17
A
SER
18
n
30
SER
18
A
LYS
19
n
31
LYS
19
A
ASN
20
n
32
ASN
20
A
LYS
21
n
33
LYS
21
A
ALA
22
n
34
ALA
22
A
VAL
23
n
35
VAL
23
A
ASP
24
n
36
ASP
24
A
VAL
25
n
37
VAL
25
A
ILE
26
n
38
ILE
26
A
GLY
27
n
39
GLY
27
A
SER
28
n
40
SER
28
A
LYS
29
n
41
LYS
29
A
LEU
30
n
42
LEU
30
A
GLY
31
n
43
GLY
31
A
GLY
32
n
44
GLY
32
A
GLN
33
n
45
GLN
33
A
VAL
34
n
46
VAL
34
A
VAL
35
n
47
VAL
35
A
SER
36
n
48
SER
36
A
PHE
37
n
49
PHE
37
A
SER
38
n
50
SER
38
A
ASP
39
n
51
ASP
39
A
GLU
40
n
52
GLU
40
A
TRP
41
n
53
TRP
41
A
PHE
42
n
54
PHE
42
A
ALA
43
n
55
ALA
43
A
SER
44
n
56
SER
44
A
ALA
45
n
57
ALA
45
A
GLU
46
n
58
GLU
46
A
ASN
47
n
59
ASN
47
A
LEU
48
n
60
LEU
48
A
ILE
49
n
61
ILE
49
A
GLN
50
n
62
GLN
50
A
PRO
51
n
63
PRO
51
A
THR
52
n
64
THR
52
A
ALA
53
n
65
ALA
53
A
PRO
54
n
66
PRO
54
A
ILE
55
n
67
ILE
55
A
ARG
56
n
68
ARG
56
A
ASP
57
n
69
ASP
57
A
n
70
58
A
n
71
59
A
n
72
60
A
n
73
61
A
n
74
62
A
n
75
63
A
n
76
64
A
n
77
65
A
n
78
66
A
TRP
67
n
79
TRP
67
A
TYR
68
n
80
TYR
68
A
ASP
69
n
81
ASP
69
A
GLY
70
n
82
GLY
70
A
TRP
71
n
83
TRP
71
A
GLU
72
n
84
GLU
72
A
THR
73
n
85
THR
73
A
ARG
74
n
86
ARG
74
A
ARG
75
n
87
ARG
75
A
HIS
76
n
88
HIS
76
A
ASN
77
n
89
ASN
77
A
GLU
78
n
90
GLU
78
A
MSE
79
n
91
MSE
79
A
GLU
80
n
92
GLU
80
A
TYR
81
n
93
TYR
81
A
ASP
82
n
94
ASP
82
A
TRP
83
n
95
TRP
83
A
VAL
84
n
96
VAL
84
A
ILE
85
n
97
ILE
85
A
ILE
86
n
98
ILE
86
A
LYS
87
n
99
LYS
87
A
MSE
88
n
100
MSE
88
A
GLY
89
n
101
GLY
89
A
VAL
90
n
102
VAL
90
A
ALA
91
n
103
ALA
91
A
ALA
92
n
104
ALA
92
A
ALA
93
n
105
ALA
93
A
HIS
94
n
106
HIS
94
A
ILE
95
n
107
ILE
95
A
ILE
96
n
108
ILE
96
A
GLY
97
n
109
GLY
97
A
GLY
98
n
110
GLY
98
A
GLU
99
n
111
GLU
99
A
ILE
100
n
112
ILE
100
A
ASP
101
n
113
ASP
101
A
THR
102
n
114
THR
102
A
ALA
103
n
115
ALA
103
A
PHE
104
n
116
PHE
104
A
PHE
105
n
117
PHE
105
A
ASN
106
n
118
ASN
106
A
GLY
107
n
119
GLY
107
A
ASN
108
n
120
ASN
108
A
HIS
109
n
121
HIS
109
A
ALA
110
n
122
ALA
110
A
PRO
111
n
123
PRO
111
A
PHE
112
n
124
PHE
112
A
VAL
113
n
125
VAL
113
A
SER
114
n
126
SER
114
A
ILE
115
n
127
ILE
115
A
GLU
116
n
128
GLU
116
A
ALA
117
n
129
ALA
117
A
LEU
118
n
130
LEU
118
A
TYR
119
n
131
TYR
119
A
ASP
120
n
132
ASP
120
A
GLU
121
n
133
GLU
121
A
GLY
122
n
134
GLY
122
A
GLU
123
n
135
GLU
123
A
GLU
124
n
136
GLU
124
A
GLY
125
n
137
GLY
125
A
ASN
126
n
138
ASN
126
A
ILE
127
n
139
ILE
127
A
VAL
128
n
140
VAL
128
A
GLU
129
n
141
GLU
129
A
ASP
130
n
142
ASP
130
A
ASP
131
n
143
ASP
131
A
SER
132
n
144
SER
132
A
ARG
133
n
145
ARG
133
A
TRP
134
n
146
TRP
134
A
VAL
135
n
147
VAL
135
A
GLU
136
n
148
GLU
136
A
ILE
137
n
149
ILE
137
A
VAL
138
n
150
VAL
138
A
GLU
139
n
151
GLU
139
A
LYS
140
n
152
LYS
140
A
PHE
141
n
153
PHE
141
A
GLU
142
n
154
GLU
142
A
CYS
143
n
155
CYS
143
A
GLY
144
n
156
GLY
144
A
PRO
145
n
157
PRO
145
A
SER
146
n
158
SER
146
A
GLN
147
n
159
GLN
147
A
ARG
148
n
160
ARG
148
A
HIS
149
n
161
HIS
149
A
LEU
150
n
162
LEU
150
A
PHE
151
n
163
PHE
151
A
VAL
152
n
164
VAL
152
A
ARG
153
n
165
ARG
153
A
GLY
154
n
166
GLY
154
A
ASN
155
n
167
ASN
155
A
GLY
156
n
168
GLY
156
A
LEU
157
n
169
LEU
157
A
THR
158
n
170
THR
158
A
LYS
159
n
171
LYS
159
A
GLU
160
n
172
GLU
160
A
ARG
161
n
173
ARG
161
A
PHE
162
n
174
PHE
162
A
THR
163
n
175
THR
163
A
HIS
164
n
176
HIS
164
A
ILE
165
n
177
ILE
165
A
LYS
166
n
178
LYS
166
A
LEU
167
n
179
LEU
167
A
LYS
168
n
180
LYS
168
A
MSE
169
n
181
MSE
169
A
TYR
170
n
182
TYR
170
A
PRO
171
n
183
PRO
171
A
ASP
172
n
184
ASP
172
A
GLY
173
n
185
GLY
173
A
GLY
174
n
186
GLY
174
A
ILE
175
n
187
ILE
175
A
ALA
176
n
188
ALA
176
A
ARG
177
n
189
ARG
177
A
PHE
178
n
190
PHE
178
A
ARG
179
n
191
ARG
179
A
LEU
180
n
192
LEU
180
A
TYR
181
n
193
TYR
181
A
GLY
182
n
194
GLY
182
A
ARG
183
n
195
ARG
183
A
VAL
184
n
196
VAL
184
A
VAL
185
n
197
VAL
185
A
PRO
186
n
198
PRO
186
A
PRO
187
n
199
PRO
187
A
n
200
188
A
n
201
189
A
n
202
190
A
n
203
191
A
n
204
192
A
n
205
193
A
HIS
194
n
206
HIS
194
A
ILE
195
n
207
ILE
195
A
ILE
196
n
208
ILE
196
A
ASP
197
n
209
ASP
197
A
LEU
198
n
210
LEU
198
A
ALA
199
n
211
ALA
199
A
TYR
200
n
212
TYR
200
A
VAL
201
n
213
VAL
201
A
CYS
202
n
214
CYS
202
A
ASN
203
n
215
ASN
203
A
GLY
204
n
216
GLY
204
A
ALA
205
n
217
ALA
205
A
VAL
206
n
218
VAL
206
A
ALA
207
n
219
ALA
207
A
LEU
208
n
220
LEU
208
A
LYS
209
n
221
LYS
209
A
TYR
210
n
222
TYR
210
A
SER
211
n
223
SER
211
A
ASP
212
n
224
ASP
212
A
GLN
213
n
225
GLN
213
A
HIS
214
n
226
HIS
214
A
PHE
215
n
227
PHE
215
A
GLY
216
n
228
GLY
216
A
SER
217
n
229
SER
217
A
VAL
218
n
230
VAL
218
A
ASP
219
n
231
ASP
219
A
ASN
220
n
232
ASN
220
A
LEU
221
n
233
LEU
221
A
LEU
222
n
234
LEU
222
A
LEU
223
n
235
LEU
223
A
PRO
224
n
236
PRO
224
A
GLY
225
n
237
GLY
225
A
ARG
226
n
238
ARG
226
A
GLY
227
n
239
GLY
227
A
HIS
228
n
240
HIS
228
A
ASP
229
n
241
ASP
229
A
MSE
230
n
242
MSE
230
A
SER
231
n
243
SER
231
A
ASP
232
n
244
ASP
232
A
GLY
233
n
245
GLY
233
A
TRP
234
n
246
TRP
234
A
GLU
235
n
247
GLU
235
A
THR
236
n
248
THR
236
A
LYS
237
n
249
LYS
237
A
ARG
238
n
250
ARG
238
A
SER
239
n
251
SER
239
A
ARG
240
n
252
ARG
240
A
GLN
241
n
253
GLN
241
A
PRO
242
n
254
PRO
242
A
GLY
243
n
255
GLY
243
A
HIS
244
n
256
HIS
244
A
THR
245
n
257
THR
245
A
ASP
246
n
258
ASP
246
A
TRP
247
n
259
TRP
247
A
ALA
248
n
260
ALA
248
A
VAL
249
n
261
VAL
249
A
ILE
250
n
262
ILE
250
A
GLN
251
n
263
GLN
251
A
LEU
252
n
264
LEU
252
A
GLY
253
n
265
GLY
253
A
ARG
254
n
266
ARG
254
A
GLU
255
n
267
GLU
255
A
SER
256
n
268
SER
256
A
SER
257
n
269
SER
257
A
PHE
258
n
270
PHE
258
A
ILE
259
n
271
ILE
259
A
GLU
260
n
272
GLU
260
A
LYS
261
n
273
LYS
261
A
ILE
262
n
274
ILE
262
A
ILE
263
n
275
ILE
263
A
VAL
264
n
276
VAL
264
A
ASP
265
n
277
ASP
265
A
THR
266
n
278
THR
266
A
ALA
267
n
279
ALA
267
A
HIS
268
n
280
HIS
268
A
PHE
269
n
281
PHE
269
A
ARG
270
n
282
ARG
270
A
GLY
271
n
283
GLY
271
A
ASN
272
n
284
ASN
272
A
PHE
273
n
285
PHE
273
A
PRO
274
n
286
PRO
274
A
GLN
275
n
287
GLN
275
A
PHE
276
n
288
PHE
276
A
ILE
277
n
289
ILE
277
A
THR
278
n
290
THR
278
A
VAL
279
n
291
VAL
279
A
GLU
280
n
292
GLU
280
A
GLY
281
n
293
GLY
281
A
CYS
282
n
294
CYS
282
A
LEU
283
n
295
LEU
283
A
LYS
284
n
296
LYS
284
A
n
297
285
A
n
298
286
A
n
299
287
A
n
300
288
A
n
301
289
A
n
302
290
A
n
303
291
A
n
304
292
A
n
305
293
A
n
306
294
A
n
307
295
A
THR
296
n
308
THR
296
A
TRP
297
n
309
TRP
297
A
VAL
298
n
310
VAL
298
A
GLU
299
n
311
GLU
299
A
LEU
300
n
312
LEU
300
A
VAL
301
n
313
VAL
301
A
GLY
302
n
314
GLY
302
A
LYS
303
n
315
LYS
303
A
SER
304
n
316
SER
304
A
LYS
305
n
317
LYS
305
A
THR
306
n
318
THR
306
A
GLY
307
n
319
GLY
307
A
PRO
308
n
320
PRO
308
A
ASP
309
n
321
ASP
309
A
LYS
310
n
322
LYS
310
A
GLU
311
n
323
GLU
311
A
HIS
312
n
324
HIS
312
A
VAL
313
n
325
VAL
313
A
TYR
314
n
326
TYR
314
A
GLU
315
n
327
GLU
315
A
ILE
316
n
328
ILE
316
A
ARG
317
n
329
ARG
317
A
LYS
318
n
330
LYS
318
A
SER
319
n
331
SER
319
A
ILE
320
n
332
ILE
320
A
ARG
321
n
333
ARG
321
A
VAL
322
n
334
VAL
322
A
SER
323
n
335
SER
323
A
HIS
324
n
336
HIS
324
A
VAL
325
n
337
VAL
325
A
LYS
326
n
338
LYS
326
A
LEU
327
n
339
LEU
327
A
THR
328
n
340
THR
328
A
ILE
329
n
341
ILE
329
A
ILE
330
n
342
ILE
330
A
PRO
331
n
343
PRO
331
A
ASP
332
n
344
ASP
332
A
GLY
333
n
345
GLY
333
A
GLY
334
n
346
GLY
334
A
VAL
335
n
347
VAL
335
A
LYS
336
n
348
LYS
336
A
ARG
337
n
349
ARG
337
A
ILE
338
n
350
ILE
338
A
ARG
339
n
351
ARG
339
A
VAL
340
n
352
VAL
340
A
TRP
341
n
353
TRP
341
A
GLY
342
n
354
GLY
342
A
TYR
343
n
355
TYR
343
A
3.3975
1.3062
-0.5912
2.0648
-0.6154
1.9452
0.0171
-0.3583
0.4264
0.3071
-0.1626
0.3068
-0.1779
-0.0122
0.1455
-0.2430
0.0106
0.0270
-0.2104
-0.0930
-0.2905
refined
31.8230
53.2820
49.0190
X-RAY DIFFRACTION
3.0547
-0.3312
-0.9740
4.7750
-0.7944
3.0036
-0.0425
-0.1506
0.0814
0.1398
0.1777
0.7001
0.0730
-0.0168
-0.1352
-0.3778
0.0183
0.0501
-0.2744
-0.0211
-0.3478
refined
15.8810
29.3240
46.2170
X-RAY DIFFRACTION
A
0
A
12
A
187
A
199
X-RAY DIFFRACTION
1
ALL
A
194
A
206
A
343
A
355
X-RAY DIFFRACTION
2
ALL
author_defined_assembly
1
monomeric
A
MSE
1
SELENOMETHIONINE
A
MSE
13
MET
A
MSE
79
SELENOMETHIONINE
A
MSE
91
MET
A
MSE
88
SELENOMETHIONINE
A
MSE
100
MET
A
MSE
169
SELENOMETHIONINE
A
MSE
181
MET
A
MSE
230
SELENOMETHIONINE
A
MSE
242
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
4
A
N
PHE
16
A
O
LEU
150
A
O
LEU
162
A
O
PHE
151
A
O
PHE
163
A
N
GLY
98
A
N
GLY
110
A
N
ASP
101
A
N
ASP
113
A
O
ARG
177
A
O
ARG
189
A
O
GLY
182
A
O
GLY
194
A
N
VAL
23
A
N
VAL
35
A
N
GLN
33
A
N
GLN
45
A
O
LYS
87
A
O
LYS
99
A
N
ILE
86
A
N
ILE
98
A
O
ILE
165
A
O
ILE
177
A
O
LYS
166
A
O
LYS
178
A
N
GLU
116
A
N
GLU
128
A
N
ILE
115
A
N
ILE
127
A
O
ILE
137
A
O
ILE
149
A
N
TRP
71
A
N
TRP
83
A
O
ILE
175
A
O
ILE
187
A
N
ILE
196
A
N
ILE
208
A
O
GLY
342
A
O
GLY
354
A
O
ARG
339
A
O
ARG
351
A
N
ILE
263
A
N
ILE
275
A
N
ILE
262
A
N
ILE
274
A
O
TYR
314
A
O
TYR
326
A
N
LYS
209
A
N
LYS
221
A
O
VAL
249
A
O
VAL
261
A
N
ILE
250
A
N
ILE
262
A
O
VAL
325
A
O
VAL
337
A
O
LYS
326
A
O
LYS
338
A
N
GLU
280
A
N
GLU
292
A
N
VAL
279
A
N
VAL
291
A
O
VAL
301
A
O
VAL
313
A
N
PHE
215
A
N
PHE
227
A
O
GLU
235
A
O
GLU
247
A
N
TRP
234
A
N
TRP
246
A
O
VAL
335
A
O
VAL
347
1
A
HOH
577
B
HOH
1
A
CE
LYS
2
A
CE
LYS
14
1
Y
1
A
NZ
LYS
2
A
NZ
LYS
14
1
Y
1
A
CE
LYS
318
A
CE
LYS
330
1
Y
1
A
NZ
LYS
318
A
NZ
LYS
330
1
Y
1
A
MET
-11
A
MET
1
1
Y
1
A
GLY
-10
A
GLY
2
1
Y
1
A
SER
-9
A
SER
3
1
Y
1
A
ASP
-8
A
ASP
4
1
Y
1
A
LYS
-7
A
LYS
5
1
Y
1
A
ILE
-6
A
ILE
6
1
Y
1
A
HIS
-5
A
HIS
7
1
Y
1
A
HIS
-4
A
HIS
8
1
Y
1
A
HIS
-3
A
HIS
9
1
Y
1
A
HIS
-2
A
HIS
10
1
Y
1
A
HIS
-1
A
HIS
11
1
Y
1
A
PRO
58
A
PRO
70
1
Y
1
A
THR
59
A
THR
71
1
Y
1
A
ARG
60
A
ARG
72
1
Y
1
A
PHE
61
A
PHE
73
1
Y
1
A
VAL
62
A
VAL
74
1
Y
1
A
HIS
63
A
HIS
75
1
Y
1
A
SER
64
A
SER
76
1
Y
1
A
GLY
65
A
GLY
77
1
Y
1
A
ALA
66
A
ALA
78
1
Y
1
A
GLU
188
A
GLU
200
1
Y
1
A
LEU
189
A
LEU
201
1
Y
1
A
LYS
190
A
LYS
202
1
Y
1
A
THR
191
A
THR
203
1
Y
1
A
LYS
192
A
LYS
204
1
Y
1
A
ASP
193
A
ASP
205
1
Y
1
A
GLU
285
A
GLU
297
1
Y
1
A
SER
286
A
SER
298
1
Y
1
A
GLU
287
A
GLU
299
1
Y
1
A
SER
288
A
SER
300
1
Y
1
A
SER
289
A
SER
301
1
Y
1
A
GLU
290
A
GLU
302
1
Y
1
A
ASN
291
A
ASN
303
1
Y
1
A
THR
292
A
THR
304
1
Y
1
A
GLY
293
A
GLY
305
1
Y
1
A
GLU
294
A
GLU
306
1
Y
1
A
GLY
295
A
GLY
307
1
Y
1
A
A
O
O
HOH
HOH
502
736
1.85
1
A
A
N
O
HIS
HOH
194
721
1.96
1
A
A
O
O
HOH
HOH
507
734
2.16
1
6.60
0.90
118.30
124.90
A
A
A
CB
CG
OD2
ASP
ASP
ASP
212
212
212
N
1
A
ILE
17
-95.84
-60.11
1
A
GLU
40
-159.81
19.42
1
A
ALA
43
-170.76
141.88
1
A
PHE
104
71.34
-2.02
1
A
ASN
106
-103.74
67.56
1
A
GLU
121
-94.18
-74.55
1
A
GLU
123
-66.57
74.33
1
A
THR
158
-37.01
133.52
1
A
ALA
267
-38.72
129.23
1
A
HIS
268
70.33
-13.55
1
A
ASN
272
-149.77
23.56
1
A
ASP
332
-173.45
-176.08
57.277
-2.40
-1.20
0.00
-2.40
0.00
3.61
0.956
0.924
1. SELENIUM OCCUPANCIES WERE SET TO 0.5, TO REFLECT VARIABLE INCORPORATION DURING EXPRESSION. THIS VALUE MINIMIZES RFREE AND THE AMOUNT OF DIFFERENCE DENSITY OVER THE SITES. 2. RESIDUES 188-193 WERE OMITTED, BECAUSE THE STRONG DIFFERENCE DENSITY REMAINED AMBIGUOUS ABOUT THE PATH OF MAIN CHAIN TRACE; THE DENSITY WAS MODELED WITH WATER. 3. THE N-TERMINUS RETAINS STRONG DIFFERENCE DENSITY, SUGGESTING A DOUBLE CONFORMATION FOR MSE1; THIS PROVED DIFFICULT TO MODEL, SO THE CONFORMATION AGREEING BEST WITH EXPERIMENTAL DENSITY WAS RETAINED. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
0.22238
0.17542
0.17765
2.40
41.97
830
17676
4.5
99.77
13.449
0.165
RANDOM
LIKELY RESIDUAL
1
ISOTROPIC
THROUGHOUT
MAD
0.279
0.215
0.80
0.80
1.20
MAXIMUM LIKELIHOOD WITH PHASES
BABINET MODEL WITH MASK
2.40
41.97
218
2766
0
0
2548
0.017
0.022
2633
0.001
0.020
2362
1.505
1.913
3554
0.832
3.000
5478
7.304
5.000
312
36.267
23.206
131
17.738
15.000
446
17.963
15.000
20
0.093
0.200
372
0.006
0.020
2920
0.001
0.020
579
0.185
0.200
479
0.199
0.200
2422
0.091
0.200
1648
0.022
0.200
1
0.148
0.200
14
0.302
0.200
46
0.164
0.200
20
0.832
1.500
1672
1.285
2.000
2531
1.706
3.000
1201
2.603
4.500
1023
0.245
2.462
0
1323
20
56.40
2.4000
54.554
1O59
18532
18532
0.099
1,2
13.0
5.1
99.8
0.707
2.40
2.46
1.8
1325
1,2
2.6
98.8
data reduction
MOSFLM
data scaling
SCALA
phasing
SOLVE
model building
RESOLVE
refinement
REFMAC
5.1.9999
data scaling
CCP4
(SCALA)
phasing
RESOLVE
Crystal structure of Allantoicase (yir029w) from Saccharomyces cerevisiae at 2.40 A resolution
1
N
N
2
N
N
A
SER
5
A
SER
17
HELX_P
A
ALA
7
A
ALA
19
5
1
3
A
ASP
8
A
ASP
20
HELX_P
A
ILE
17
A
ILE
29
1
2
10
A
GLY
27
A
GLY
39
HELX_P
A
GLY
31
A
GLY
43
5
3
5
A
SER
44
A
SER
56
HELX_P
A
GLN
50
A
GLN
62
5
4
7
A
TYR
200
A
TYR
212
HELX_P
A
GLY
204
A
GLY
216
5
5
5
A
VAL
218
A
VAL
230
HELX_P
A
LEU
223
A
LEU
235
5
6
6
A
ASP
229
A
ASP
241
HELX_P
A
ASP
232
A
ASP
244
5
7
4
covale
1.336
both
A
HIS
0
A
C
HIS
12
1_555
A
MSE
1
A
N
MSE
13
1_555
covale
1.332
both
A
MSE
1
A
C
MSE
13
1_555
A
LYS
2
A
N
LYS
14
1_555
covale
1.329
both
A
GLU
78
A
C
GLU
90
1_555
A
MSE
79
A
N
MSE
91
1_555
covale
1.333
both
A
MSE
79
A
C
MSE
91
1_555
A
GLU
80
A
N
GLU
92
1_555
covale
1.330
both
A
LYS
87
A
C
LYS
99
1_555
A
MSE
88
A
N
MSE
100
1_555
covale
1.330
both
A
MSE
88
A
C
MSE
100
1_555
A
GLY
89
A
N
GLY
101
1_555
covale
1.327
both
A
LYS
168
A
C
LYS
180
1_555
A
MSE
169
A
N
MSE
181
1_555
covale
1.327
both
A
MSE
169
A
C
MSE
181
1_555
A
TYR
170
A
N
TYR
182
1_555
covale
1.335
both
A
ASP
229
A
C
ASP
241
1_555
A
MSE
230
A
N
MSE
242
1_555
covale
1.316
both
A
MSE
230
A
C
MSE
242
1_555
A
SER
231
A
N
SER
243
1_555
HYDROLASE
YIR029W, ALLANTOICASE, STRUCTURAL GENOMICS, JCSG, PSI, Protein Structure Initiative, Joint Center for Structural Genomics, HYDROLASE
A
TYR
170
A
TYR
182
1
A
PRO
171
A
PRO
183
0.04
A
ILE
330
A
ILE
342
1
A
PRO
331
A
PRO
343
-16.11
ALC_YEAST
UNP
1
1
P25335
MKFFSLADEAEFKSIIISKNKAVDVIGSKLGGQVVSFSDEWFASAENLIQPTAPIRDPTRFVHSGAWYDGWETRRHNEME
YDWVIIKMGVAAAHIIGGEIDTAFFNGNHAPFVSIEALYDEGEEGNIVEDDSRWVEIVEKFECGPSQRHLFVRGNGLTKE
RFTHIKLKMYPDGGIARFRLYGRVVPPELKTKDHIIDLAYVCNGAVALKYSDQHFGSVDNLLLPGRGHDMSDGWETKRSR
QPGHTDWAVIQLGRESSFIEKIIVDTAHFRGNFPQFITVEGCLKESESSENTGEGTWVELVGKSKTGPDKEHVYEIRKSI
RVSHVKLTIIPDGGVKRIRVWGY
1
343
1O59
1
343
P25335
A
1
13
355
1
expression tag
GLY
-10
1O59
A
P25335
UNP
2
1
expression tag
SER
-9
1O59
A
P25335
UNP
3
1
expression tag
ASP
-8
1O59
A
P25335
UNP
4
1
expression tag
LYS
-7
1O59
A
P25335
UNP
5
1
expression tag
ILE
-6
1O59
A
P25335
UNP
6
1
expression tag
HIS
-5
1O59
A
P25335
UNP
7
1
expression tag
HIS
-4
1O59
A
P25335
UNP
8
1
expression tag
HIS
-3
1O59
A
P25335
UNP
9
1
expression tag
HIS
-2
1O59
A
P25335
UNP
10
1
expression tag
HIS
-1
1O59
A
P25335
UNP
11
1
expression tag
HIS
0
1O59
A
P25335
UNP
12
1
MET
modified residue
MSE
1
1O59
A
P25335
UNP
1
13
1
MET
modified residue
MSE
79
1O59
A
P25335
UNP
79
91
1
MET
modified residue
MSE
88
1O59
A
P25335
UNP
88
100
1
MET
modified residue
MSE
169
1O59
A
P25335
UNP
169
181
1
MET
modified residue
MSE
230
1O59
A
P25335
UNP
230
242
5
5
2
4
5
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
2
A
LYS
14
A
PHE
4
A
PHE
16
A
ARG
148
A
ARG
160
A
VAL
152
A
VAL
164
A
ALA
93
A
ALA
105
A
ASP
101
A
ASP
113
A
ARG
177
A
ARG
189
A
VAL
184
A
VAL
196
A
VAL
23
A
VAL
35
A
ASP
24
A
ASP
36
A
GLN
33
A
GLN
45
A
PHE
37
A
PHE
49
A
ASP
82
A
ASP
94
A
LYS
87
A
LYS
99
A
HIS
164
A
HIS
176
A
TYR
170
A
TYR
182
A
PHE
112
A
PHE
124
A
LEU
118
A
LEU
130
A
VAL
135
A
VAL
147
A
GLU
142
A
GLU
154
A
TRP
71
A
TRP
83
A
GLU
72
A
GLU
84
A
GLY
174
A
GLY
186
A
ILE
175
A
ILE
187
A
ILE
196
A
ILE
208
A
ASP
197
A
ASP
209
A
ARG
337
A
ARG
349
A
TYR
343
A
TYR
355
A
PHE
258
A
PHE
270
A
ASP
265
A
ASP
277
A
GLU
311
A
GLU
323
A
SER
319
A
SER
331
A
VAL
206
A
VAL
218
A
TYR
210
A
TYR
222
A
ASP
246
A
ASP
258
A
GLN
251
A
GLN
263
A
HIS
324
A
HIS
336
A
ILE
330
A
ILE
342
A
PHE
276
A
PHE
288
A
CYS
282
A
CYS
294
A
TRP
297
A
TRP
309
A
LYS
305
A
LYS
317
A
PHE
215
A
PHE
227
A
GLY
216
A
GLY
228
A
TRP
234
A
TRP
246
A
GLU
235
A
GLU
247
A
GLY
334
A
GLY
346
A
VAL
335
A
VAL
347
182
P 63 2 2