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3MFL
Biol. Unit 1
Info
Asym.Unit (243 KB)
Biol.Unit 1 (935 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
:
02 Apr 10 (Deposition) - 13 Apr 11 (Release) - 13 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.78
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, Intradiol, Substrate Analogue, 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
(5, 68)
Info
All Hetero Components
1a: BETA-MERCAPTOETHANOL (BMEa)
1b: BETA-MERCAPTOETHANOL (BMEb)
1c: BETA-MERCAPTOETHANOL (BMEc)
2a: CHLORIDE ION (CLa)
3a: CARBONATE ION (CO3a)
4a: 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID (DHYa)
4b: 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID (DHYb)
4c: 2-(3,4-DIHYDROXYPHENYL)ACETIC ACID (DHYc)
5a: FE (III) ION (FEa)
5b: FE (III) ION (FEb)
5c: FE (III) ION (FEc)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
7a: SULFATE ION (SO4a)
7b: SULFATE ION (SO4b)
7c: SULFATE ION (SO4c)
7d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
12
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
CO3
4
Ligand/Ion
CARBONATE ION
4
DHY
12
Ligand/Ion
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
5
FE
-1
Ligand/Ion
FE (III) ION
6
GOL
24
Ligand/Ion
GLYCEROL
7
SO4
16
Ligand/Ion
SULFATE ION
[
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Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107
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:901
BINDING SITE FOR RESIDUE GOL A 202
03
AC3
SOFTWARE
ARG A:38 , LEU A:39 , LYS A:41 , LEU A:85 , ASN A:87 , ALA A:88 , ASN A:90
BINDING SITE FOR RESIDUE GOL A 203
04
AC4
SOFTWARE
PRO A:164 , HOH A:255
BINDING SITE FOR RESIDUE BME A 204
05
AC5
SOFTWARE
TYR M:408 , HIS M:447 , HIS M:460 , TYR M:462 , DHY M:539
BINDING SITE FOR RESIDUE FE M 600
06
AC6
SOFTWARE
ARG M:383
BINDING SITE FOR RESIDUE CO3 M 1
07
AC7
SOFTWARE
PRO A:15 , TYR A:16 , ARG A:133 , HOH A:232 , TYR M:408 , HIS M:447 , PRO M:448 , TRP M:449 , ARG M:457 , HIS M:460 , TYR M:462 , HOH M:579 , FE M:600 , HOH M:808 , HOH M:907 , HOH M:916
BINDING SITE FOR RESIDUE DHY M 539
08
AC8
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107
BINDING SITE FOR RESIDUE SO4 B 201
09
AC9
SOFTWARE
GLU B:168 , THR B:169 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188 , HOH B:883
BINDING SITE FOR RESIDUE GOL B 202
10
BC1
SOFTWARE
LEU B:23 , ASN B:28 , PRO B:29 , HOH B:742 , PHE N:367
BINDING SITE FOR RESIDUE BME B 203
11
BC2
SOFTWARE
GLU B:69 , ASN B:127 , ILE B:128 , SER B:129 , HIS B:140 , HOH B:249 , ILE N:470
BINDING SITE FOR RESIDUE BME B 204
12
BC3
SOFTWARE
TYR N:408 , HIS N:447 , HIS N:460 , TYR N:462 , DHY N:539
BINDING SITE FOR RESIDUE FE N 600
13
BC4
SOFTWARE
ARG N:383 , ASP N:434 , HOH N:723
BINDING SITE FOR RESIDUE SO4 N 4
14
BC5
SOFTWARE
GLN N:503 , ILE N:505 , ARG N:522 , PHE N:523 , ASP N:524
BINDING SITE FOR RESIDUE GOL N 1
15
BC6
SOFTWARE
PRO B:15 , TYR B:16 , HOH B:894 , TYR N:408 , HIS N:447 , TRP N:449 , ARG N:450 , ARG N:457 , HIS N:460 , TYR N:462 , FE N:600 , HOH N:756 , HOH N:897 , HOH N:917 , HOH N:1023 , HOH N:1037
BINDING SITE FOR RESIDUE DHY N 539
16
BC7
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107 , HOH C:990
BINDING SITE FOR RESIDUE SO4 C 201
17
BC8
SOFTWARE
THR C:169 , ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188 , HOH C:955 , HOH C:1048
BINDING SITE FOR RESIDUE GOL C 202
18
BC9
SOFTWARE
TYR O:408 , HIS O:447 , HIS O:460 , TYR O:462 , DHY O:540
BINDING SITE FOR RESIDUE FE O 600
19
CC1
SOFTWARE
GLN O:503 , ILE O:505 , LYS O:507 , ARG O:522 , PHE O:523 , ASP O:524
BINDING SITE FOR RESIDUE GOL O 1
20
CC2
SOFTWARE
PRO C:15 , TYR C:16 , TYR O:408 , HIS O:447 , TRP O:449 , ARG O:450 , ARG O:457 , HIS O:460 , TYR O:462 , FE O:600 , HOH O:768 , HOH O:770 , HOH O:887 , HOH O:914 , HOH O:1022
BINDING SITE FOR RESIDUE DHY O 540
[
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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_d3mfla_ (A:)
1b: SCOP_d3mflb_ (B:)
1c: SCOP_d3mflc_ (C:)
2a: SCOP_d3mflm_ (M:)
2b: SCOP_d3mfln_ (N:)
2c: SCOP_d3mflo_ (O:)
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(
)
Folds
(
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(
)
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)
(
)
Families
(
)
(
)
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
d3mfla_
A:
1b
d3mflb_
B:
1c
d3mflc_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3mflm_
M:
2b
d3mfln_
N:
2c
d3mflo_
O:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 9)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_3mflC01 (C:23-192)
1b: PFAM_Dioxygenase_C_3mflC02 (C:23-192)
1c: PFAM_Dioxygenase_C_3mflC03 (C:23-192)
1d: PFAM_Dioxygenase_C_3mflO01 (O:346-530)
1e: PFAM_Dioxygenase_C_3mflO02 (O:346-530)
1f: PFAM_Dioxygenase_C_3mflO03 (O:346-530)
2a: PFAM_PCDO_beta_N_3mflO04 (O:308-343)
2b: PFAM_PCDO_beta_N_3mflO05 (O:308-343)
2c: PFAM_PCDO_beta_N_3mflO06 (O:308-343)
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-3mflC01
C:23-192
1b
Dioxygenase_C-3mflC02
C:23-192
1c
Dioxygenase_C-3mflC03
C:23-192
1d
Dioxygenase_C-3mflO01
O:346-530
1e
Dioxygenase_C-3mflO02
O:346-530
1f
Dioxygenase_C-3mflO03
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-3mflO04
O:308-343
2b
PCDO_beta_N-3mflO05
O:308-343
2c
PCDO_beta_N-3mflO06
O:308-343
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