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Asym. Unit
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (305 KB)
Biol.Unit 2 (308 KB)
Biol.Unit 3 (309 KB)
Biol.Unit 4 (310 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE FROM BURKHOLDERIA XENOVORANS LB400
Authors
:
P. Kumar, J. T. Bolin
Date
:
12 Sep 10 (Deposition) - 24 Nov 10 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: S,T,U,V,W,X (1x)
Biol. Unit 4: M,N,O,P,Q,R (1x)
Keywords
:
Oxidoreductase, Degradation, Bpdo
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Kumar, M. Mohammadi, J. F. Viger, D. Barriault, L. Gomez-Gil, L. D. Eltis, J. T. Bolin, M. Sylvestre
Structural Insight Into The Expanded Pcb-Degrading Abilities Of A Biphenyl Dioxygenase Obtained By Directed Evolution.
J. Mol. Biol. V. 405 531 2011
[
close entry info
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Hetero Components
(2, 24)
Info
All Hetero Components
1a: FE (II) ION (FE2a)
1b: FE (II) ION (FE2b)
1c: FE (II) ION (FE2c)
1d: FE (II) ION (FE2d)
1e: FE (II) ION (FE2e)
1f: FE (II) ION (FE2f)
1g: FE (II) ION (FE2g)
1h: FE (II) ION (FE2h)
1i: FE (II) ION (FE2i)
1j: FE (II) ION (FE2j)
1k: FE (II) ION (FE2k)
1l: FE (II) ION (FE2l)
2a: FE2/S2 (INORGANIC) CLUSTER (FESa)
2b: FE2/S2 (INORGANIC) CLUSTER (FESb)
2c: FE2/S2 (INORGANIC) CLUSTER (FESc)
2d: FE2/S2 (INORGANIC) CLUSTER (FESd)
2e: FE2/S2 (INORGANIC) CLUSTER (FESe)
2f: FE2/S2 (INORGANIC) CLUSTER (FESf)
2g: FE2/S2 (INORGANIC) CLUSTER (FESg)
2h: FE2/S2 (INORGANIC) CLUSTER (FESh)
2i: FE2/S2 (INORGANIC) CLUSTER (FESi)
2j: FE2/S2 (INORGANIC) CLUSTER (FESj)
2k: FE2/S2 (INORGANIC) CLUSTER (FESk)
2l: FE2/S2 (INORGANIC) CLUSTER (FESl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE2
12
Ligand/Ion
FE (II) ION
2
FES
12
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:100 , HIS A:102 , ARG A:103 , CYS A:120 , HIS A:123 , TRP A:125
BINDING SITE FOR RESIDUE FES A 900
02
AC2
SOFTWARE
GLN A:226 , HIS A:233 , HIS A:239 , ASP A:388 , HOH A:2023
BINDING SITE FOR RESIDUE FE2 A 901
03
AC3
SOFTWARE
CYS C:100 , HIS C:102 , ARG C:103 , CYS C:120 , HIS C:123 , TRP C:125
BINDING SITE FOR RESIDUE FES C 900
04
AC4
SOFTWARE
GLN C:226 , HIS C:233 , HIS C:239 , ASP C:388 , HOH C:2017
BINDING SITE FOR RESIDUE FE2 C 901
05
AC5
SOFTWARE
CYS E:100 , HIS E:102 , ARG E:103 , CYS E:120 , HIS E:123 , TRP E:125
BINDING SITE FOR RESIDUE FES E 900
06
AC6
SOFTWARE
GLN E:226 , HIS E:233 , HIS E:239 , ASP E:388 , HOH E:2019
BINDING SITE FOR RESIDUE FE2 E 901
07
AC7
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
08
AC8
SOFTWARE
GLN G:226 , HIS G:233 , HIS G:239 , ASP G:388 , HOH G:2021
BINDING SITE FOR RESIDUE FE2 G 901
09
AC9
SOFTWARE
CYS I:100 , HIS I:102 , ARG I:103 , MET I:105 , CYS I:120 , HIS I:123 , TRP I:125
BINDING SITE FOR RESIDUE FES I 900
10
BC1
SOFTWARE
GLN I:226 , HIS I:233 , HIS I:239 , ASP I:388 , HOH I:2021
BINDING SITE FOR RESIDUE FE2 I 901
11
BC2
SOFTWARE
CYS K:100 , HIS K:102 , ARG K:103 , MET K:105 , CYS K:120 , HIS K:123 , TRP K:125
BINDING SITE FOR RESIDUE FES K 900
12
BC3
SOFTWARE
HIS K:233 , HIS K:239 , ASP K:388 , HOH K:2042
BINDING SITE FOR RESIDUE FE2 K 901
13
BC4
SOFTWARE
CYS M:100 , HIS M:102 , ARG M:103 , CYS M:120 , HIS M:123 , TRP M:125
BINDING SITE FOR RESIDUE FES M 900
14
BC5
SOFTWARE
HIS M:233 , HIS M:239 , ASP M:388 , HOH M:2027
BINDING SITE FOR RESIDUE FE2 M 901
15
BC6
SOFTWARE
CYS O:100 , HIS O:102 , ARG O:103 , CYS O:120 , HIS O:123 , TRP O:125
BINDING SITE FOR RESIDUE FES O 900
16
BC7
SOFTWARE
GLN O:226 , HIS O:233 , HIS O:239 , ASP O:388 , HOH O:2044
BINDING SITE FOR RESIDUE FE2 O 901
17
BC8
SOFTWARE
CYS Q:100 , HIS Q:102 , ARG Q:103 , CYS Q:120 , HIS Q:123 , TRP Q:125
BINDING SITE FOR RESIDUE FES Q 900
18
BC9
SOFTWARE
GLN Q:226 , HIS Q:233 , HIS Q:239 , ASP Q:388 , HOH Q:2037
BINDING SITE FOR RESIDUE FE2 Q 901
19
CC1
SOFTWARE
CYS S:100 , HIS S:102 , ARG S:103 , CYS S:120 , HIS S:123 , TRP S:125
BINDING SITE FOR RESIDUE FES S 900
20
CC2
SOFTWARE
GLN S:226 , HIS S:233 , HIS S:239 , ASP S:388 , HOH S:2014
BINDING SITE FOR RESIDUE FE2 S 901
21
CC3
SOFTWARE
CYS U:100 , HIS U:102 , ARG U:103 , CYS U:120 , TYR U:122 , HIS U:123 , TRP U:125
BINDING SITE FOR RESIDUE FES U 900
22
CC4
SOFTWARE
GLN U:226 , HIS U:233 , HIS U:239 , ASP U:388 , HOH U:2019
BINDING SITE FOR RESIDUE FE2 U 901
23
CC5
SOFTWARE
CYS W:100 , HIS W:102 , ARG W:103 , CYS W:120 , HIS W:123 , TRP W:125
BINDING SITE FOR RESIDUE FES W 900
24
CC6
SOFTWARE
GLN W:226 , HIS W:233 , HIS W:239 , ASP W:388 , HOH W:2010
BINDING SITE FOR RESIDUE FE2 W 901
[
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
(2, 24)
Info
All PROSITE Patterns/Profiles
1: RIESKE (A:58-140,C:58-140,E:58-140,G:58-14...)
2: RING_HYDROXYL_ALPHA (A:100-123,C:100-123,E:100-123,G:10...)
;
View:
Select:
Label:
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
12
A:58-140
C:58-140
E:58-140
G:58-140
I:58-140
K:58-140
M:58-140
O:58-140
Q:58-140
S:58-140
U:58-140
W:58-140
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
BPHA_PARXL
100-123
12
A:100-123
C:100-123
E:100-123
G:100-123
I:100-123
K:100-123
M:100-123
O:100-123
Q:100-123
S:100-123
U:100-123
W:100-123
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 36)
Info
All SCOP Domains
1a: SCOP_d2xr8a1 (A:18-179)
1b: SCOP_d2xr8c1 (C:18-179)
1c: SCOP_d2xr8e1 (E:18-179)
1d: SCOP_d2xr8g1 (G:18-179)
1e: SCOP_d2xr8i1 (I:18-179)
1f: SCOP_d2xr8k1 (K:18-179)
1g: SCOP_d2xr8m1 (M:18-179)
1h: SCOP_d2xr8o1 (O:18-179)
1i: SCOP_d2xr8q1 (Q:18-179)
1j: SCOP_d2xr8s1 (S:18-179)
1k: SCOP_d2xr8u1 (U:18-179)
1l: SCOP_d2xr8w1 (W:18-179)
2a: SCOP_d2xr8b_ (B:)
2b: SCOP_d2xr8d_ (D:)
2c: SCOP_d2xr8f_ (F:)
2d: SCOP_d2xr8h_ (H:)
2e: SCOP_d2xr8j_ (J:)
2f: SCOP_d2xr8l_ (L:)
2g: SCOP_d2xr8n_ (N:)
2h: SCOP_d2xr8p_ (P:)
2i: SCOP_d2xr8r_ (R:)
2j: SCOP_d2xr8t_ (T:)
2k: SCOP_d2xr8v_ (V:)
2l: SCOP_d2xr8x_ (X:)
3a: SCOP_d2xr8a2 (A:180-459)
3b: SCOP_d2xr8c2 (C:180-459)
3c: SCOP_d2xr8e2 (E:180-459)
3d: SCOP_d2xr8g2 (G:180-459)
3e: SCOP_d2xr8i2 (I:180-459)
3f: SCOP_d2xr8k2 (K:180-459)
3g: SCOP_d2xr8m2 (M:180-459)
3h: SCOP_d2xr8o2 (O:180-459)
3i: SCOP_d2xr8q2 (Q:180-459)
3j: SCOP_d2xr8s2 (S:180-459)
3k: SCOP_d2xr8u2 (U:180-459)
3l: SCOP_d2xr8w2 (W:180-459)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d2xr8a1
A:18-179
1b
d2xr8c1
C:18-179
1c
d2xr8e1
E:18-179
1d
d2xr8g1
G:18-179
1e
d2xr8i1
I:18-179
1f
d2xr8k1
K:18-179
1g
d2xr8m1
M:18-179
1h
d2xr8o1
O:18-179
1i
d2xr8q1
Q:18-179
1j
d2xr8s1
S:18-179
1k
d2xr8u1
U:18-179
1l
d2xr8w1
W: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
d2xr8b_
B:
2b
d2xr8d_
D:
2c
d2xr8f_
F:
2d
d2xr8h_
H:
2e
d2xr8j_
J:
2f
d2xr8l_
L:
2g
d2xr8n_
N:
2h
d2xr8p_
P:
2i
d2xr8r_
R:
2j
d2xr8t_
T:
2k
d2xr8v_
V:
2l
d2xr8x_
X:
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
automated matches
(39)
Protein domain
:
automated matches
(39)
Burkholderia xenovorans [TaxId: 266265]
(7)
3a
d2xr8a2
A:180-459
3b
d2xr8c2
C:180-459
3c
d2xr8e2
E:180-459
3d
d2xr8g2
G:180-459
3e
d2xr8i2
I:180-459
3f
d2xr8k2
K:180-459
3g
d2xr8m2
M:180-459
3h
d2xr8o2
O:180-459
3i
d2xr8q2
Q:180-459
3j
d2xr8s2
S:180-459
3k
d2xr8u2
U:180-459
3l
d2xr8w2
W:180-459
[
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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
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
[
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Chain J
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Asym.Unit (1.2 MB)
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Biol.Unit 1 (305 KB)
Header - Biol.Unit 1
Biol.Unit 2 (308 KB)
Header - Biol.Unit 2
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