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3T63
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
:
28 Jul 11 (Deposition) - 01 Aug 12 (Release) - 01 Aug 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.54
Chains
:
Asym. Unit : A,B,C,M,N,O
Biol. Unit 1: A,B,C,M,N,O (4x)
Keywords
:
Iron Iii Dependent Non-Heme Intradiol Dioxygenase, 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
[
close entry info
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Hetero Components
(3, 80)
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)
1l: BETA-MERCAPTOETHANOL (BMEl)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BME
48
Ligand/Ion
BETA-MERCAPTOETHANOL
2
FE
-1
Ligand/Ion
FE (III) ION
3
GOL
16
Ligand/Ion
GLYCEROL
4
SO4
16
Ligand/Ion
SULFATE ION
[
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Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:56 , ASP A:57 , GLY A:60 , ARG A:188 , ILE A:189 , GLN A:190 , GLY A:191 , GLU A:192
BINDING SITE FOR RESIDUE BME A 201
02
AC2
SOFTWARE
GLU A:168 , THR A:169 , LEU A:170 , ILE A:171 , ARG A:184 , PHE A:185 , ASP A:186 , ARG A:188 , HOH A:955
BINDING SITE FOR RESIDUE GOL A 202
03
AC3
SOFTWARE
ASN A:37 , THR A:105 , HIS A:107 , HOH A:682
BINDING SITE FOR RESIDUE SO4 A 203
04
AC4
SOFTWARE
GLU B:168 , THR B:169 , ILE B:171 , ARG B:184 , PHE B:185 , ASP B:186 , ARG B:188
BINDING SITE FOR RESIDUE GOL B 201
05
AC5
SOFTWARE
ASN B:37 , ARG B:38 , THR B:105 , HIS B:107
BINDING SITE FOR RESIDUE SO4 B 202
06
AC6
SOFTWARE
THR C:169 , ILE C:171 , ARG C:184 , PHE C:185 , ASP C:186 , ARG C:188 , HOH C:954 , HOH C:1492
BINDING SITE FOR RESIDUE GOL C 201
07
AC7
SOFTWARE
ASN C:37 , THR C:105 , HIS C:107
BINDING SITE FOR RESIDUE SO4 C 202
08
AC8
SOFTWARE
TYR M:408 , ARG M:457 , HIS M:460 , TYR M:462 , BME M:542 , FE M:600 , HOH M:613 , HOH M:1559
BINDING SITE FOR RESIDUE BME M 1
09
AC9
SOFTWARE
PHE M:356 , CYS M:429 , LEU M:430 , HOH M:568
BINDING SITE FOR RESIDUE BME M 539
10
BC1
SOFTWARE
ARG M:450 , PRO M:453 , HOH M:1460 , HOH M:1545 , HOH N:145 , SER N:338 , ILE N:339 , PRO N:340
BINDING SITE FOR RESIDUE BME M 540
11
BC2
SOFTWARE
GLN M:503 , ILE M:505 , ARG M:522 , PHE M:523 , ASP M:524
BINDING SITE FOR RESIDUE GOL M 541
12
BC3
SOFTWARE
ARG M:383
BINDING SITE FOR RESIDUE SO4 M 7
13
BC4
SOFTWARE
PRO A:15 , ARG A:133 , HOH A:1482 , BME M:1 , HOH M:296 , TYR M:324 , THR M:326 , TRP M:449 , HOH M:1488
BINDING SITE FOR RESIDUE BME M 542
14
BC5
SOFTWARE
PHE A:200 , ILE M:310 , ILE M:339 , PRO M:340 , GLN M:341 , HOH M:547 , PRO O:453 , PRO O:515
BINDING SITE FOR RESIDUE BME M 543
15
BC6
SOFTWARE
BME M:1 , TYR M:408 , HIS M:460 , TYR M:462 , HOH M:1559
BINDING SITE FOR RESIDUE FE M 600
16
BC7
SOFTWARE
TYR B:16 , TYR N:408 , ARG N:457 , TYR N:462 , BME N:540 , HOH N:577 , FE N:600 , HOH N:1560
BINDING SITE FOR RESIDUE BME N 1
17
BC8
SOFTWARE
PHE N:356 , CYS N:429 , LEU N:430 , HOH N:700 , HOH N:1102
BINDING SITE FOR RESIDUE BME N 539
18
BC9
SOFTWARE
PRO B:15 , ARG B:133 , BME N:1 , HOH N:65 , TYR N:324 , THR N:326 , TRP N:449 , HOH N:1484 , HOH N:1536
BINDING SITE FOR RESIDUE BME N 540
19
CC1
SOFTWARE
BME N:1 , TYR N:408 , HIS N:460 , TYR N:462 , HOH N:1560
BINDING SITE FOR RESIDUE FE N 600
20
CC2
SOFTWARE
TYR C:16 , TYR O:408 , TRP O:449 , ARG O:457 , HIS O:460 , TYR O:462 , BME O:539 , BME O:540 , FE O:600 , HOH O:654 , HOH O:1561 , HOH O:1566
BINDING SITE FOR RESIDUE BME O 1
21
CC3
SOFTWARE
PRO C:15 , BME O:1 , TRP O:449 , ARG O:450 , BME O:540 , HOH O:1566
BINDING SITE FOR RESIDUE BME O 539
22
CC4
SOFTWARE
PRO C:15 , ARG C:133 , BME O:1 , HOH O:143 , TYR O:324 , THR O:326 , TRP O:449 , BME O:539
BINDING SITE FOR RESIDUE BME O 540
23
CC5
SOFTWARE
BME O:1 , TYR O:408 , HIS O:460 , TYR O:462 , HOH O:1561
BINDING SITE FOR RESIDUE FE O 600
[
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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:
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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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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_d3t63a_ (A:)
1b: SCOP_d3t63b_ (B:)
1c: SCOP_d3t63c_ (C:)
2a: SCOP_d3t63m_ (M:)
2b: SCOP_d3t63n_ (N:)
2c: SCOP_d3t63o_ (O:)
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Protein Domains
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)
(
)
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
d3t63a_
A:
1b
d3t63b_
B:
1c
d3t63c_
C:
Protein domain
:
Protocatechuate-3,4-dioxygenase, beta chain
(44)
Pseudomonas putida [TaxId: 303]
(31)
2a
d3t63m_
M:
2b
d3t63n_
N:
2c
d3t63o_
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
(0, 0)
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all PFAM domains
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Sorry, no Info available
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Chain M
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Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
Asymmetric Unit 4
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
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