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2YFJ
Biol. Unit 2
Info
Asym.Unit (601 KB)
Biol.Unit 1 (305 KB)
Biol.Unit 2 (297 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE VARIANT RR41 WITH DIBENZOFURAN
Authors
:
P. Kumar, M. Sylvestre, J. T. Bolin
Date
:
06 Apr 11 (Deposition) - 08 Jun 11 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.15
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Keywords
:
Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Mohammadi, J. Viger, P. Kumar, D. Barriault, J. T. Bolin, M. Sylvestre
Retuning Rieske-Type Oxygenases To Expand Substrate Range.
J. Biol. Chem. V. 286 27612 2011
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: DIBENZOFURAN (1ITa)
1b: DIBENZOFURAN (1ITb)
1c: DIBENZOFURAN (1ITc)
2a: FE (II) ION (FE2a)
2b: FE (II) ION (FE2b)
2c: FE (II) ION (FE2c)
2d: FE (II) ION (FE2d)
2e: FE (II) ION (FE2e)
2f: FE (II) ION (FE2f)
3a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3b: FE2/S2 (INORGANIC) CLUSTER (FESb)
3c: FE2/S2 (INORGANIC) CLUSTER (FESc)
3d: FE2/S2 (INORGANIC) CLUSTER (FESd)
3e: FE2/S2 (INORGANIC) CLUSTER (FESe)
3f: FE2/S2 (INORGANIC) CLUSTER (FESf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
1IT
-1
Ligand/Ion
DIBENZOFURAN
2
FE2
3
Ligand/Ion
FE (II) ION
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
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Sites
(6, 6)
Info
All Sites
1: BC1 (SOFTWARE)
2: BC2 (SOFTWARE)
3: BC3 (SOFTWARE)
4: BC4 (SOFTWARE)
5: BC5 (SOFTWARE)
6: BC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
BC1
SOFTWARE
CYS G:100 , HIS G:102 , ARG G:103 , CYS G:120 , HIS G:123 , TRP G:125
BINDING SITE FOR RESIDUE FES G 900
2
BC2
SOFTWARE
GLN G:226 , HIS G:233 , HIS G:239 , ASP G:388 , HOH G:2020
BINDING SITE FOR RESIDUE FE2 G 901
3
BC3
SOFTWARE
CYS I:100 , HIS I:102 , ARG I:103 , CYS I:120 , HIS I:123 , TRP I:125
BINDING SITE FOR RESIDUE FES I 900
4
BC4
SOFTWARE
GLN I:226 , HIS I:233 , HIS I:239 , ASP I:388 , HOH I:2018
BINDING SITE FOR RESIDUE FE2 I 901
5
BC5
SOFTWARE
CYS K:100 , HIS K:102 , ARG K:103 , CYS K:120 , HIS K:123 , TRP K:125
BINDING SITE FOR RESIDUE FES K 900
6
BC6
SOFTWARE
GLN K:226 , HIS K:233 , HIS K:239 , ASP K:388 , HOH K:2016
BINDING SITE FOR RESIDUE FE2 K 901
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RIESKE (G:58-140,I:58-140,K:58-140)
2: RING_HYDROXYL_ALPHA (G:100-123,I:100-123,K:100-123)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RIESKE
PS51296
Rieske [2Fe-2S] iron-sulfur domain profile.
BPHA_PARXL
58-140
3
-
-
-
G:58-140
I:58-140
K:58-140
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
BPHA_PARXL
100-123
3
-
-
-
G:100-123
I:100-123
K:100-123
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Exons
(0, 0)
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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
(3, 18)
Info
All SCOP Domains
1a: SCOP_d2yfja1 (A:18-179)
1b: SCOP_d2yfji1 (I:18-179)
1c: SCOP_d2yfjk1 (K:18-179)
1d: SCOP_d2yfjc1 (C:18-179)
1e: SCOP_d2yfje1 (E:18-179)
1f: SCOP_d2yfjg1 (G:18-179)
2a: SCOP_d2yfjb_ (B:)
2b: SCOP_d2yfjj_ (J:)
2c: SCOP_d2yfjl_ (L:)
2d: SCOP_d2yfjd_ (D:)
2e: SCOP_d2yfjf_ (F:)
2f: SCOP_d2yfjh_ (H:)
3a: SCOP_d2yfja2 (A:180-459)
3b: SCOP_d2yfji2 (I:180-459)
3c: SCOP_d2yfjk2 (K:180-459)
3d: SCOP_d2yfjc2 (C:180-459)
3e: SCOP_d2yfje2 (E:180-459)
3f: SCOP_d2yfjg2 (G:180-459)
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)
Protein Domains
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)
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)
Organisms
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Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
automated matches
(22)
Protein domain
:
automated matches
(22)
Burkholderia xenovorans [TaxId: 266265]
(7)
1a
d2yfja1
A:18-179
1b
d2yfji1
I:18-179
1c
d2yfjk1
K:18-179
1d
d2yfjc1
C:18-179
1e
d2yfje1
E:18-179
1f
d2yfjg1
G:18-179
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
automated matches
(12)
Burkholderia xenovorans [TaxId: 266265]
(7)
2a
d2yfjb_
B:
2b
d2yfjj_
J:
2c
d2yfjl_
L:
2d
d2yfjd_
D:
2e
d2yfjf_
F:
2f
d2yfjh_
H:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Burkholderia xenovorans [TaxId: 266265]
(7)
3a
d2yfja2
A:180-459
3b
d2yfji2
I:180-459
3c
d2yfjk2
K:180-459
3d
d2yfjc2
C:180-459
3e
d2yfje2
E:180-459
3f
d2yfjg2
G:180-459
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CATH Domains
(0, 0)
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (601 KB)
Header - Asym.Unit
Biol.Unit 1 (305 KB)
Header - Biol.Unit 1
Biol.Unit 2 (297 KB)
Header - Biol.Unit 2
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