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3MI1
Biol. Unit 1
Info
Asym.Unit (250 KB)
Biol.Unit 1 (962 KB)
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(1)
Title
:
AXIAL LIGAND SWAPPING IN DOUBLE MUTANT MAINTAINS INTRADIOL-CLEAVAGE CHEMISTRY IN PROTOCATECHUATE 3,4-DIOXYGENASE
Authors
:
V. M. Purpero, J. D. Lipscomb
Date
:
09 Apr 10 (Deposition) - 27 Apr 11 (Release) - 27 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.74
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Dioxygenase, Non-Heme, Iron, Homoprotocatechuate, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. M. Purpero, J. D. Lipscomb
Axial Ligand Swapping In Double Mutant Maintains Intradiol-Cleavage Chemistry In Protocatechuate 3, 4-Dioxygenase
To Be Published
[
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Hetero Components
(3, 92)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
1d: BETA-MERCAPTOETHANOL (BMEd)
1e: BETA-MERCAPTOETHANOL (BMEe)
1f: BETA-MERCAPTOETHANOL (BMEf)
1g: BETA-MERCAPTOETHANOL (BMEg)
1h: BETA-MERCAPTOETHANOL (BMEh)
1i: BETA-MERCAPTOETHANOL (BMEi)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
4e: GLYCEROL (GOLe)
4f: GLYCEROL (GOLf)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
36
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
FE
-1
Ligand/Ion
FE (III) ION
4
GOL
24
Ligand/Ion
GLYCEROL
5
SO4
32
Ligand/Ion
SULFATE ION
[
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Sites
(28, 28)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107 , HOH A:258 , HOH A:631
BINDING SITE FOR RESIDUE SO4 A 201
02
AC2
SOFTWARE
THR A:169 , ILE A:171 , ARG A:184 , PHE A:185 , ASP A:186 , ARG A:188 , HOH A:235 , HOH A:885 , HOH A:1033
BINDING SITE FOR RESIDUE GOL A 202
03
AC3
SOFTWARE
THR A:12 , GLY A:14 , HOH A:1055 , ARG M:457 , TYR M:462 , GLN M:477 , HOH M:1067
BINDING SITE FOR RESIDUE FE M 600
04
AC4
SOFTWARE
ARG A:133 , HOH A:1055 , HOH A:1084 , HOH A:1163 , TYR M:324 , THR M:326 , TRP M:449 , HOH M:552
BINDING SITE FOR RESIDUE SO4 A 203
05
AC5
SOFTWARE
ILE B:2 , GLN M:503 , LYS M:507 , ARG M:522 , PHE M:523 , ASP M:524
BINDING SITE FOR RESIDUE GOL M 1
06
AC6
SOFTWARE
ARG M:409 , PRO M:421
BINDING SITE FOR RESIDUE BME M 541
07
AC7
SOFTWARE
PHE M:535 , HIS O:361
BINDING SITE FOR RESIDUE BME M 542
08
AC8
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107 , HOH B:450
BINDING SITE FOR RESIDUE SO4 B 201
09
AC9
SOFTWARE
ARG B:133 , HOH B:557 , HOH B:1060 , HOH N:226 , TYR N:324 , THR N:326 , TRP N:449 , HOH N:1198
BINDING SITE FOR RESIDUE SO4 B 202
10
BC1
SOFTWARE
THR B:12 , GLY B:14 , HOH B:1060 , ARG N:457 , TYR N:462 , GLN N:477 , HOH N:1077
BINDING SITE FOR RESIDUE FE N 600
11
BC2
SOFTWARE
ARG N:414 , ARG N:450 , HOH N:1219
BINDING SITE FOR RESIDUE SO4 N 8
12
BC3
SOFTWARE
GLN N:503 , ILE N:505 , LYS N:507 , ARG N:522 , PHE N:523 , ASP N:524
BINDING SITE FOR RESIDUE GOL N 539
13
BC4
SOFTWARE
ARG N:407 , LEU N:419
BINDING SITE FOR RESIDUE BME N 540
14
BC5
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107 , HOH C:669
BINDING SITE FOR RESIDUE SO4 C 201
15
BC6
SOFTWARE
ARG C:133 , HOH C:665 , HOH C:1058 , HOH C:1242 , HOH O:236 , TYR O:324 , THR O:326 , TRP O:449
BINDING SITE FOR RESIDUE SO4 C 202
16
BC7
SOFTWARE
THR C:169 , ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188 , HOH C:673 , HOH C:1028
BINDING SITE FOR RESIDUE GOL C 203
17
BC8
SOFTWARE
PRO C:164 , ARG C:167 , HOH C:679
BINDING SITE FOR RESIDUE BME C 204
18
BC9
SOFTWARE
LEU C:23 , ASN C:28 , PRO C:29 , HOH C:530 , PHE O:367
BINDING SITE FOR RESIDUE BME C 205
19
CC1
SOFTWARE
THR C:12 , GLY C:14 , HOH C:1058 , ARG O:457 , TYR O:462 , GLN O:477 , HOH O:1078
BINDING SITE FOR RESIDUE FE O 600
20
CC2
SOFTWARE
GLN O:503 , ILE O:505 , ARG O:522 , PHE O:523 , ASP O:524
BINDING SITE FOR RESIDUE GOL O 1
21
CC3
SOFTWARE
ARG O:407 , LEU O:419
BINDING SITE FOR RESIDUE BME O 539
22
CC4
SOFTWARE
THR O:321 , PRO O:322 , ASP O:323 , LYS O:493 , HOH O:551
BINDING SITE FOR RESIDUE BME O 540
23
CC5
SOFTWARE
ARG O:383
BINDING SITE FOR RESIDUE CL O 541
24
CC6
SOFTWARE
GLU B:168 , THR B:169 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188 , HOH B:564 , HOH B:973
BINDING SITE FOR RESIDUE GOL B 203
25
CC7
SOFTWARE
ASN O:412 , ARG O:414 , ARG O:450
BINDING SITE FOR RESIDUE SO4 O 3
26
CC8
SOFTWARE
HOH M:87 , ARG M:407 , LEU M:419
BINDING SITE FOR RESIDUE CL M 540
27
CC9
SOFTWARE
HIS N:534 , PHE N:535 , GLU N:536
BINDING SITE FOR RESIDUE BME N 1
28
DC1
SOFTWARE
HIS O:534 , PHE O:535
BINDING SITE FOR RESIDUE BME O 542
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 24)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (M:380-408,N:380-408,O:380-408)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTRADIOL_DIOXYGENAS
PS00083
Intradiol ring-cleavage dioxygenases signature.
PCXA_PSEPU
52-80
12
A:51-79
B:51-79
C:51-79
PCXB_PSEPU
81-109
12
M:380-408
N:380-408
O:380-408
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3mi1a_ (A:)
1b: SCOP_d3mi1b_ (B:)
1c: SCOP_d3mi1c_ (C:)
2a: SCOP_d3mi1m_ (M:)
2b: SCOP_d3mi1n_ (N:)
2c: SCOP_d3mi1o_ (O:)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
Aromatic compound dioxygenase
(100)
Protein domain
:
Protocatechuate-3,4-dioxygenase, alpha chain
(37)
Pseudomonas putida [TaxId: 303]
(31)
1a
d3mi1a_
A:
1b
d3mi1b_
B:
1c
d3mi1c_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3mi1m_
M:
2b
d3mi1n_
N:
2c
d3mi1o_
O:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(2, 9)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_3mi1C01 (C:23-192)
1b: PFAM_Dioxygenase_C_3mi1C02 (C:23-192)
1c: PFAM_Dioxygenase_C_3mi1C03 (C:23-192)
1d: PFAM_Dioxygenase_C_3mi1O01 (O:346-530)
1e: PFAM_Dioxygenase_C_3mi1O02 (O:346-530)
1f: PFAM_Dioxygenase_C_3mi1O03 (O:346-530)
2a: PFAM_PCDO_beta_N_3mi1O04 (O:308-343)
2b: PFAM_PCDO_beta_N_3mi1O05 (O:308-343)
2c: PFAM_PCDO_beta_N_3mi1O06 (O:308-343)
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Clans
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(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-3mi1C01
C:23-192
1b
Dioxygenase_C-3mi1C02
C:23-192
1c
Dioxygenase_C-3mi1C03
C:23-192
1d
Dioxygenase_C-3mi1O01
O:346-530
1e
Dioxygenase_C-3mi1O02
O:346-530
1f
Dioxygenase_C-3mi1O03
O:346-530
Clan
:
no clan defined [family: PCDO_beta_N]
(26)
Family
:
PCDO_beta_N
(26)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(26)
2a
PCDO_beta_N-3mi1O04
O:308-343
2b
PCDO_beta_N-3mi1O05
O:308-343
2c
PCDO_beta_N-3mi1O06
O:308-343
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