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1H0M
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (87 KB)
Biol.Unit 2 (85 KB)
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(1)
Title
:
THREE-DIMENSIONAL STRUCTURE OF THE QUORUM SENSING PROTEIN TRAR BOUND TO ITS AUTOINDUCER AND TO ITS TARGET DNA
Authors
:
A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. Cortese, R. De Fra P. Neddermann, S. Di Marco
Date
:
25 Jun 02 (Deposition) - 29 Aug 02 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,E,F (1x)
Biol. Unit 2: C,D,G,H (1x)
Keywords
:
Transcription/Dna, Luxr-Type Protein, Quorum Sensing, Transcriptional Regulator, Dna-Binding Protein, Homoserine Lactone, Trar, Transcription-Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Vannini, C. Volpari, C. Gargioli, E. Muraglia, R. Cortese, R. De Francesco, P. Neddermann, S. Di Marco
The Crystal Structure Of The Quorum Sensing Protein Trar Bound To Its Autoinducer And Target Dna
Embo J. V. 21 4393 2002
(for further references see the
PDB file header
)
[
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]
Hetero Components
(3, 31)
Info
All Hetero Components
1a: HOMOSERINE LACTONE (HSLa)
1b: HOMOSERINE LACTONE (HSLb)
1c: HOMOSERINE LACTONE (HSLc)
1d: HOMOSERINE LACTONE (HSLd)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
2i: SELENOMETHIONINE (MSEi)
2j: SELENOMETHIONINE (MSEj)
2k: SELENOMETHIONINE (MSEk)
2l: SELENOMETHIONINE (MSEl)
2m: SELENOMETHIONINE (MSEm)
2n: SELENOMETHIONINE (MSEn)
2o: SELENOMETHIONINE (MSEo)
2p: SELENOMETHIONINE (MSEp)
2q: SELENOMETHIONINE (MSEq)
2r: SELENOMETHIONINE (MSEr)
2s: SELENOMETHIONINE (MSEs)
2t: SELENOMETHIONINE (MSEt)
2u: SELENOMETHIONINE (MSEu)
2v: SELENOMETHIONINE (MSEv)
2w: SELENOMETHIONINE (MSEw)
3a: 3-OXOOCTANOIC ACID (OOAa)
3b: 3-OXOOCTANOIC ACID (OOAb)
3c: 3-OXOOCTANOIC ACID (OOAc)
3d: 3-OXOOCTANOIC ACID (OOAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HSL
4
Ligand/Ion
HOMOSERINE LACTONE
2
MSE
23
Mod. Amino Acid
SELENOMETHIONINE
3
OOA
4
Ligand/Ion
3-OXOOCTANOIC ACID
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TRP A:57 , TYR A:61 , ASP A:70 , VAL A:72 , PHE A:101 , TYR A:102 , ALA A:105 , ILE A:110 , OOA A:1236
BINDING SITE FOR RESIDUE HSL A1235
2
AC2
SOFTWARE
LEU A:40 , TYR A:53 , GLN A:58 , TYR A:61 , ASP A:70 , VAL A:72 , MSE A:127 , HSL A:1235
BINDING SITE FOR RESIDUE OOA A1236
3
AC3
SOFTWARE
TRP B:57 , TYR B:61 , ASP B:70 , VAL B:72 , TRP B:85 , PHE B:101 , TYR B:102 , ALA B:105 , ILE B:110 , OOA B:1236
BINDING SITE FOR RESIDUE HSL B1235
4
AC4
SOFTWARE
LEU B:40 , TYR B:53 , GLN B:58 , TYR B:61 , PHE B:62 , ASP B:70 , THR B:129 , HSL B:1235
BINDING SITE FOR RESIDUE OOA B1236
5
AC5
SOFTWARE
TYR C:53 , TRP C:57 , ASP C:70 , VAL C:72 , PHE C:101 , ALA C:105 , ILE C:110 , OOA C:1236
BINDING SITE FOR RESIDUE HSL C1235
6
AC6
SOFTWARE
LEU C:40 , TYR C:53 , TYR C:61 , VAL C:72 , TRP C:85 , MSE C:127 , THR C:129 , HSL C:1235
BINDING SITE FOR RESIDUE OOA C1236
7
AC7
SOFTWARE
TRP D:57 , TYR D:61 , ASP D:70 , VAL D:72 , TRP D:85 , ALA D:105 , ILE D:110 , OOA D:1236
BINDING SITE FOR RESIDUE HSL D1235
8
AC8
SOFTWARE
ALA D:38 , LEU D:40 , TYR D:53 , TYR D:61 , TRP D:85 , THR D:129 , HSL D:1235
BINDING SITE FOR RESIDUE OOA D1236
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: HTH_LUXR_2 (A:170-232,B:167-232,C:171-232,D:16...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_LUXR_2
PS50043
LuxR-type HTH domain profile.
TRAR_RHIRD
167-232
4
A:170-232
B:167-232
C:171-232
D:167-232
[
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1h0ma1 (A:170-234)
1b: SCOP_d1h0mb1 (B:170-234)
1c: SCOP_d1h0mc1 (C:171-234)
1d: SCOP_d1h0md1 (D:170-234)
2a: SCOP_d1h0ma2 (A:1-165)
2b: SCOP_d1h0mb2 (B:1-169)
2c: SCOP_d1h0mc2 (C:1-164)
2d: SCOP_d1h0md2 (D:2-169)
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(
)
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)
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(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
C-terminal effector domain of the bipartite response regulators
(45)
Family
:
GerE-like (LuxR/UhpA family of transcriptional regulators)
(11)
Protein domain
:
Quorum-sensing transcription factor TraR, C-terminal domain
(2)
Agrobacterium tumefaciens [TaxId: 358]
(2)
1a
d1h0ma1
A:170-234
1b
d1h0mb1
B:170-234
1c
d1h0mc1
C:171-234
1d
d1h0md1
D:170-234
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Profilin-like
(304)
Superfamily
:
Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
(2)
Family
:
Pheromone-binding domain of LuxR-like quorum-sensing transcription factors
(2)
Protein domain
:
Transcription factor TraR, N-terminal domain
(2)
Agrobacterium tumefaciens [TaxId: 358]
(2)
2a
d1h0ma2
A:1-165
2b
d1h0mb2
B:1-169
2c
d1h0mc2
C:1-164
2d
d1h0md2
D:2-169
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1h0mB01 (B:2-171)
1b: CATH_1h0mD01 (D:2-171)
1c: CATH_1h0mA01 (A:2-170)
1d: CATH_1h0mC01 (C:2-180)
2a: CATH_1h0mA02 (A:171-234)
2b: CATH_1h0mB02 (B:172-234)
2c: CATH_1h0mD02 (D:172-234)
2d: CATH_1h0mC02 (C:181-234)
View:
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(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Beta-Lactamase
(202)
Homologous Superfamily
:
[code=3.30.450.80, no name defined]
(2)
Agrobacterium tumefaciens. Organism_taxid: 358. Strain: a348.
(1)
1a
1h0mB01
B:2-171
1b
1h0mD01
D:2-171
1c
1h0mA01
A:2-170
1d
1h0mC01
C:2-180
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
Agrobacterium tumefaciens. Organism_taxid: 358. Strain: a348.
(1)
2a
1h0mA02
A:171-234
2b
1h0mB02
B:172-234
2c
1h0mD02
D:172-234
2d
1h0mC02
C:181-234
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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