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2XRX
Biol. Unit 3
Info
Asym.Unit (1.2 MB)
Biol.Unit 1 (308 KB)
Biol.Unit 2 (308 KB)
Biol.Unit 3 (314 KB)
Biol.Unit 4 (309 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF BIPHENYL DIOXYGENASE IN COMPLEX WITH BIPHENYL FROM BURKHOLDERIA XENOVORANS LB400
Authors
:
P. Kumar, J. T. Bolin
Date
:
23 Sep 10 (Deposition) - 24 Nov 10 (Release) - 16 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.42
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: M,N,O,P,Q,R (1x)
Biol. Unit 4: S,T,U,V,W,X (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
(3, 9)
Info
All Hetero Components
1a: BIPHENYL (BNLa)
1b: BIPHENYL (BNLb)
1c: BIPHENYL (BNLc)
1d: BIPHENYL (BNLd)
1e: BIPHENYL (BNLe)
1f: BIPHENYL (BNLf)
1g: BIPHENYL (BNLg)
1h: BIPHENYL (BNLh)
1i: BIPHENYL (BNLi)
1j: BIPHENYL (BNLj)
1k: BIPHENYL (BNLk)
1l: BIPHENYL (BNLl)
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)
2g: FE (II) ION (FE2g)
2h: FE (II) ION (FE2h)
2i: FE (II) ION (FE2i)
2j: FE (II) ION (FE2j)
2k: FE (II) ION (FE2k)
2l: FE (II) ION (FE2l)
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)
3g: FE2/S2 (INORGANIC) CLUSTER (FESg)
3h: FE2/S2 (INORGANIC) CLUSTER (FESh)
3i: FE2/S2 (INORGANIC) CLUSTER (FESi)
3j: FE2/S2 (INORGANIC) CLUSTER (FESj)
3k: FE2/S2 (INORGANIC) CLUSTER (FESk)
3l: FE2/S2 (INORGANIC) CLUSTER (FESl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BNL
3
Ligand/Ion
BIPHENYL
2
FE2
3
Ligand/Ion
FE (II) ION
3
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: CC1 (SOFTWARE)
2: CC2 (SOFTWARE)
3: CC3 (SOFTWARE)
4: CC4 (SOFTWARE)
5: CC5 (SOFTWARE)
6: CC6 (SOFTWARE)
7: CC7 (SOFTWARE)
8: CC8 (SOFTWARE)
9: CC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
CC1
SOFTWARE
CYS M:100 , HIS M:102 , ARG M:103 , CYS M:120 , TYR M:122 , HIS M:123 , TRP M:125
BINDING SITE FOR RESIDUE FES M1460
2
CC2
SOFTWARE
GLN M:226 , HIS M:233 , HIS M:239 , ASP M:388 , HOH M:2034
BINDING SITE FOR RESIDUE FE2 M1461
3
CC3
SOFTWARE
GLN M:226 , ASP M:230 , MET M:231 , HIS M:233 , GLY M:321 , HIS M:323 , LEU M:333 , PHE M:336 , PHE M:384
BINDING SITE FOR RESIDUE BNL M1462
4
CC4
SOFTWARE
CYS O:100 , HIS O:102 , ARG O:103 , CYS O:120 , HIS O:123 , TRP O:125
BINDING SITE FOR RESIDUE FES O1460
5
CC5
SOFTWARE
GLN O:226 , HIS O:233 , HIS O:239 , ASP O:388 , HOH O:2053
BINDING SITE FOR RESIDUE FE2 O1461
6
CC6
SOFTWARE
GLN O:226 , ASP O:230 , HIS O:233 , GLY O:321 , HIS O:323 , LEU O:333 , PHE O:336
BINDING SITE FOR RESIDUE BNL O1462
7
CC7
SOFTWARE
CYS Q:100 , HIS Q:102 , ARG Q:103 , CYS Q:120 , HIS Q:123 , TRP Q:125
BINDING SITE FOR RESIDUE FES Q1460
8
CC8
SOFTWARE
GLN Q:226 , HIS Q:233 , HIS Q:239 , ASP Q:388 , HOH Q:2048
BINDING SITE FOR RESIDUE FE2 Q1461
9
CC9
SOFTWARE
GLN Q:226 , ASP Q:230 , HIS Q:233 , HIS Q:323 , LEU Q:333 , HOH Q:2048
BINDING SITE FOR RESIDUE BNL Q1462
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: RIESKE (M:58-140,O:58-140,Q:58-140)
2: RING_HYDROXYL_ALPHA (M:100-123,O:100-123,Q:100-123)
;
View:
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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
3
-
-
-
-
-
-
M:58-140
O:58-140
Q:58-140
-
-
-
2
RING_HYDROXYL_ALPHA
PS00570
Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
BPHA_PARXL
100-123
3
-
-
-
-
-
-
M:100-123
O:100-123
Q:100-123
-
-
-
[
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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
(3, 36)
Info
All SCOP Domains
1a: SCOP_d2xrxa1 (A:18-179)
1b: SCOP_d2xrxc1 (C:18-179)
1c: SCOP_d2xrxe1 (E:18-179)
1d: SCOP_d2xrxg1 (G:18-179)
1e: SCOP_d2xrxi1 (I:18-179)
1f: SCOP_d2xrxk1 (K:18-179)
1g: SCOP_d2xrxm1 (M:18-179)
1h: SCOP_d2xrxo1 (O:18-179)
1i: SCOP_d2xrxq1 (Q:18-179)
1j: SCOP_d2xrxs1 (S:18-179)
1k: SCOP_d2xrxu1 (U:18-179)
1l: SCOP_d2xrxw1 (W:18-179)
2a: SCOP_d2xrxb_ (B:)
2b: SCOP_d2xrxd_ (D:)
2c: SCOP_d2xrxf_ (F:)
2d: SCOP_d2xrxh_ (H:)
2e: SCOP_d2xrxj_ (J:)
2f: SCOP_d2xrxl_ (L:)
2g: SCOP_d2xrxn_ (N:)
2h: SCOP_d2xrxp_ (P:)
2i: SCOP_d2xrxr_ (R:)
2j: SCOP_d2xrxt_ (T:)
2k: SCOP_d2xrxv_ (V:)
2l: SCOP_d2xrxx_ (X:)
3a: SCOP_d2xrxa2 (A:180-459)
3b: SCOP_d2xrxc2 (C:180-459)
3c: SCOP_d2xrxe2 (E:180-459)
3d: SCOP_d2xrxg2 (G:180-459)
3e: SCOP_d2xrxi2 (I:180-459)
3f: SCOP_d2xrxk2 (K:180-459)
3g: SCOP_d2xrxm2 (M:180-459)
3h: SCOP_d2xrxo2 (O:180-459)
3i: SCOP_d2xrxq2 (Q:180-459)
3j: SCOP_d2xrxs2 (S:180-459)
3k: SCOP_d2xrxu2 (U:180-459)
3l: SCOP_d2xrxw2 (W:180-459)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
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(
)
(
)
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
d2xrxa1
A:18-179
1b
d2xrxc1
C:18-179
1c
d2xrxe1
E:18-179
1d
d2xrxg1
G:18-179
1e
d2xrxi1
I:18-179
1f
d2xrxk1
K:18-179
1g
d2xrxm1
M:18-179
1h
d2xrxo1
O:18-179
1i
d2xrxq1
Q:18-179
1j
d2xrxs1
S:18-179
1k
d2xrxu1
U:18-179
1l
d2xrxw1
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
d2xrxb_
B:
2b
d2xrxd_
D:
2c
d2xrxf_
F:
2d
d2xrxh_
H:
2e
d2xrxj_
J:
2f
d2xrxl_
L:
2g
d2xrxn_
N:
2h
d2xrxp_
P:
2i
d2xrxr_
R:
2j
d2xrxt_
T:
2k
d2xrxv_
V:
2l
d2xrxx_
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
d2xrxa2
A:180-459
3b
d2xrxc2
C:180-459
3c
d2xrxe2
E:180-459
3d
d2xrxg2
G:180-459
3e
d2xrxi2
I:180-459
3f
d2xrxk2
K:180-459
3g
d2xrxm2
M:180-459
3h
d2xrxo2
O:180-459
3i
d2xrxq2
Q:180-459
3j
d2xrxs2
S:180-459
3k
d2xrxu2
U:180-459
3l
d2xrxw2
W:180-459
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (1.2 MB)
Header - Asym.Unit
Biol.Unit 1 (308 KB)
Header - Biol.Unit 1
Biol.Unit 2 (308 KB)
Header - Biol.Unit 2
Biol.Unit 3 (314 KB)
Header - Biol.Unit 3
Biol.Unit 4 (309 KB)
Header - Biol.Unit 4
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