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3MV4
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (1002 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
:
03 May 10 (Deposition) - 01 Jun 11 (Release) - 01 Jun 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.59
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Intradiol, Non-Heme, Holoenzyme, Ferric Iron, 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, 32)
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)
1j: BETA-MERCAPTOETHANOL (BMEj)
1k: BETA-MERCAPTOETHANOL (BMEk)
2a: CARBONATE ION (CO3a)
2b: CARBONATE ION (CO3b)
2c: CARBONATE ION (CO3c)
2d: CARBONATE ION (CO3d)
2e: CARBONATE ION (CO3e)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
11
Ligand/Ion
BETA-MERCAPTOETHANOL
2
CO3
5
Ligand/Ion
CARBONATE ION
3
FE
3
Ligand/Ion
FE (III) ION
4
GOL
6
Ligand/Ion
GLYCEROL
5
SO4
7
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(32, 32)
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)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107 , HOH A:705
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:1110 , HOH A:1316
BINDING SITE FOR RESIDUE GOL A 0
03
AC3
SOFTWARE
TYR A:56 , ASP A:57 , GLY A:60 , ARG A:188 , GLN A:190 , GLY A:191 , GLU A:192 , HOH A:1108
BINDING SITE FOR RESIDUE BME A 202
04
AC4
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107
BINDING SITE FOR RESIDUE SO4 B 201
05
AC5
SOFTWARE
ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , HOH B:1367
BINDING SITE FOR RESIDUE GOL B 202
06
AC6
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107 , HOH C:833 , HOH C:1031
BINDING SITE FOR RESIDUE SO4 C 201
07
AC7
SOFTWARE
GLU C:168 , THR C:169 , ILE C:171 , ALA C:172 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188 , HOH C:1197 , HOH C:1490
BINDING SITE FOR RESIDUE GOL C 202
08
AC8
SOFTWARE
ARG M:414 , ARG M:450 , HOH M:1283
BINDING SITE FOR RESIDUE SO4 M 6
09
AC9
SOFTWARE
ARG M:409 , LEU M:419 , PRO M:421 , HOH M:567
BINDING SITE FOR RESIDUE GOL M 2
10
BC1
SOFTWARE
TYR M:408 , HIS M:447 , HIS M:460 , TYR M:462 , CO3 M:543
BINDING SITE FOR RESIDUE FE M 600
11
BC2
SOFTWARE
GLN M:503 , ILE M:505 , LYS M:507 , ARG M:522 , PHE M:523 , ASP M:524
BINDING SITE FOR RESIDUE GOL M 1
12
BC3
SOFTWARE
ARG A:31 , ASP M:360 , ASN M:366 , VAL M:426 , GLY M:427
BINDING SITE FOR RESIDUE BME M 539
13
BC4
SOFTWARE
PHE M:356 , CYS M:429 , LEU M:430 , HOH M:587
BINDING SITE FOR RESIDUE BME M 540
14
BC5
SOFTWARE
PRO A:15 , ARG A:133 , HOH M:220 , TYR M:324 , THR M:326 , TRP M:449 , ILE M:491 , CO3 M:543
BINDING SITE FOR RESIDUE BME M 541
15
BC6
SOFTWARE
GLY M:482 , GLN M:502 , ILE M:505 , LYS M:507 , HOH M:797
BINDING SITE FOR RESIDUE BME M 542
16
BC7
SOFTWARE
TYR A:16 , HOH M:220 , TYR M:408 , HIS M:447 , ARG M:457 , HIS M:460 , TYR M:462 , BME M:541 , FE M:600 , HOH M:1450
BINDING SITE FOR RESIDUE CO3 M 543
17
BC8
SOFTWARE
ARG N:409 , PRO N:421 , HOH N:586
BINDING SITE FOR RESIDUE SO4 N 4
18
BC9
SOFTWARE
ARG M:383
BINDING SITE FOR RESIDUE SO4 N 5
19
CC1
SOFTWARE
GLU A:176 , HOH N:296 , PHE N:356 , CYS N:429 , LEU N:430 , HOH N:611 , HOH N:940
BINDING SITE FOR RESIDUE BME N 1
20
CC2
SOFTWARE
TYR N:408 , HIS N:447 , HIS N:460 , TYR N:462 , CO3 N:542
BINDING SITE FOR RESIDUE FE N 600
21
CC3
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
22
CC4
SOFTWARE
HOH N:257 , ARG N:450 , HOH O:225 , SER O:338
BINDING SITE FOR RESIDUE CO3 N 540
23
CC5
SOFTWARE
ILE M:328 , ARG N:333 , HOH N:721 , HOH N:928
BINDING SITE FOR RESIDUE CO3 N 541
24
CC6
SOFTWARE
TYR B:16 , HOH N:82 , TYR N:408 , HIS N:447 , ARG N:457 , HIS N:460 , TYR N:462 , FE N:600 , HOH N:1451 , HOH N:1555
BINDING SITE FOR RESIDUE CO3 N 542
25
CC7
SOFTWARE
PRO B:15 , ARG B:133 , HOH N:82 , TYR N:324 , THR N:326 , TRP N:449 , HOH N:1555
BINDING SITE FOR RESIDUE BME N 543
26
CC8
SOFTWARE
HIS N:534 , PHE N:535 , GLU N:536 , HOH N:1084
BINDING SITE FOR RESIDUE BME N 544
27
CC9
SOFTWARE
ARG O:409 , LEU O:419 , PRO O:421 , HOH O:543
BINDING SITE FOR RESIDUE SO4 O 7
28
DC1
SOFTWARE
CO3 O:1 , TYR O:408 , HIS O:447 , HIS O:460 , TYR O:462
BINDING SITE FOR RESIDUE FE O 600
29
DC2
SOFTWARE
TYR C:16 , HOH O:172 , TYR O:408 , HIS O:447 , ARG O:457 , HIS O:460 , TYR O:462 , FE O:600 , HOH O:1086 , HOH O:1563
BINDING SITE FOR RESIDUE CO3 O 1
30
DC3
SOFTWARE
GLY C:14 , PRO C:15 , ARG C:133 , HOH O:172 , TYR O:324 , THR O:326 , TRP O:449 , HOH O:1563
BINDING SITE FOR RESIDUE BME O 539
31
DC4
SOFTWARE
SER N:438 , HIS O:534 , PHE O:535
BINDING SITE FOR RESIDUE BME O 540
32
DC5
SOFTWARE
ARG C:31 , ASP C:32 , HOH C:1579 , GLY O:357 , ASP O:360 , HOH O:608
BINDING SITE FOR RESIDUE BME O 541
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: INTRADIOL_DIOXYGENAS (A:51-79,B:51-79,C:51-79,M: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
3
A:51-79
B:51-79
C:51-79
PCXB_PSEPU
81-109
3
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.
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d3mv4a_ (A:)
1b: SCOP_d3mv4b_ (B:)
1c: SCOP_d3mv4c_ (C:)
2a: SCOP_d3mv4m_ (M:)
2b: SCOP_d3mv4n_ (N:)
2c: SCOP_d3mv4o_ (O:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d3mv4a_
A:
1b
d3mv4b_
B:
1c
d3mv4c_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3mv4m_
M:
2b
d3mv4n_
N:
2c
d3mv4o_
O:
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
[
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Pfam Domains
(2, 9)
Info
all PFAM domains
1a: PFAM_Dioxygenase_C_3mv4C01 (C:23-192)
1b: PFAM_Dioxygenase_C_3mv4C02 (C:23-192)
1c: PFAM_Dioxygenase_C_3mv4C03 (C:23-192)
1d: PFAM_Dioxygenase_C_3mv4O01 (O:346-530)
1e: PFAM_Dioxygenase_C_3mv4O02 (O:346-530)
1f: PFAM_Dioxygenase_C_3mv4O03 (O:346-530)
2a: PFAM_PCDO_beta_N_3mv4O04 (O:308-343)
2b: PFAM_PCDO_beta_N_3mv4O05 (O:308-343)
2c: PFAM_PCDO_beta_N_3mv4O06 (O:308-343)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Dioxygenase_C
(32)
Pseudomonas putida (Arthrobacter siderocapsulatus)
(27)
1a
Dioxygenase_C-3mv4C01
C:23-192
1b
Dioxygenase_C-3mv4C02
C:23-192
1c
Dioxygenase_C-3mv4C03
C:23-192
1d
Dioxygenase_C-3mv4O01
O:346-530
1e
Dioxygenase_C-3mv4O02
O:346-530
1f
Dioxygenase_C-3mv4O03
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-3mv4O04
O:308-343
2b
PCDO_beta_N-3mv4O05
O:308-343
2c
PCDO_beta_N-3mv4O06
O:308-343
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