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1U8R
Biol. Unit 2
Info
Asym.Unit (345 KB)
Biol.Unit 1 (171 KB)
Biol.Unit 2 (170 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN IDER-DNA COMPLEX REVEALS A CONFORMATIONAL CHANGE IN ACTIVATED IDER FOR BASE-SPECIFIC INTERACTIONS
Authors
:
G. Wisedchaisri, R. K. Holmes, W. G. J. Hol
Date
:
06 Aug 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
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
:
Ider, Iron-Dependent Regulator, Iron Acquisition, Siderophores, Mycobacterium Tuberculosis, Metal-Binding Protein, Transcription/Dna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Wisedchaisri, R. K. Holmes, W. G. J. Hol
Crystal Structure Of An Ider-Dna Complex Reveals A Conformational Change In Activated Ider For Base-Specific Interactions.
J. Mol. Biol. V. 342 1155 2004
(for further references see the
PDB file header
)
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: COBALT (II) ION (COa)
1b: COBALT (II) ION (COb)
1c: COBALT (II) ION (COc)
1d: COBALT (II) ION (COd)
1e: COBALT (II) ION (COe)
1f: COBALT (II) ION (COf)
1g: COBALT (II) ION (COg)
1h: COBALT (II) ION (COh)
1i: COBALT (II) ION (COi)
1j: COBALT (II) ION (COj)
1k: COBALT (II) ION (COk)
1l: COBALT (II) ION (COl)
1m: COBALT (II) ION (COm)
1n: COBALT (II) ION (COn)
1o: COBALT (II) ION (COo)
1p: COBALT (II) ION (COp)
1q: COBALT (II) ION (COq)
1r: COBALT (II) ION (COr)
1s: COBALT (II) ION (COs)
1t: COBALT (II) ION (COt)
1u: COBALT (II) ION (COu)
1v: COBALT (II) ION (COv)
1w: COBALT (II) ION (COw)
1x: COBALT (II) ION (COx)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
2c: SODIUM ION (NAc)
2d: SODIUM ION (NAd)
2e: SODIUM ION (NAe)
2f: SODIUM ION (NAf)
2g: SODIUM ION (NAg)
2h: SODIUM ION (NAh)
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Sites
(16, 16)
Info
All Sites
01: BC4 (SOFTWARE)
02: BC5 (SOFTWARE)
03: BC6 (SOFTWARE)
04: BC7 (SOFTWARE)
05: BC8 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
13: DC2 (SOFTWARE)
14: DC3 (SOFTWARE)
15: DC4 (SOFTWARE)
16: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC4
SOFTWARE
HIS G:79 , GLU G:83 , HIS G:98 , GLU G:172 , GLN G:175
BINDING SITE FOR RESIDUE CO G 5001
02
BC5
SOFTWARE
MET G:10 , CYS G:102 , GLU G:105 , HIS G:106
BINDING SITE FOR RESIDUE CO G 5002
03
BC6
SOFTWARE
HIS G:219 , HIS G:223 , HOH G:5107
BINDING SITE FOR RESIDUE CO G 5003
04
BC7
SOFTWARE
HIS H:79 , GLU H:83 , HIS H:98 , GLU H:172 , GLN H:175
BINDING SITE FOR RESIDUE CO H 6001
05
BC8
SOFTWARE
MET H:10 , CYS H:102 , GLU H:105 , HIS H:106
BINDING SITE FOR RESIDUE CO H 6002
06
BC9
SOFTWARE
HIS H:219 , HIS H:223 , HOH H:6108
BINDING SITE FOR RESIDUE CO H 6003
07
CC1
SOFTWARE
HIS I:79 , GLU I:83 , HIS I:98 , GLU I:172 , GLN I:175
BINDING SITE FOR RESIDUE CO I 7001
08
CC2
SOFTWARE
MET I:10 , CYS I:102 , GLU I:105 , HIS I:106
BINDING SITE FOR RESIDUE CO I 7002
09
CC3
SOFTWARE
HIS I:219 , HIS I:223 , HOH I:7111
BINDING SITE FOR RESIDUE CO I 7003
10
CC4
SOFTWARE
HIS J:79 , GLU J:83 , HIS J:98 , GLU J:172 , GLN J:175
BINDING SITE FOR RESIDUE CO J 8001
11
CC5
SOFTWARE
MET J:10 , CYS J:102 , GLU J:105 , HIS J:106
BINDING SITE FOR RESIDUE CO J 8002
12
CC6
SOFTWARE
HIS J:219 , HIS J:223 , HOH J:8109
BINDING SITE FOR RESIDUE CO J 8003
13
DC2
SOFTWARE
ASP G:35 , DC L:19 , HOH L:35 , HOH L:42
BINDING SITE FOR RESIDUE NA G 5105
14
DC3
SOFTWARE
ASP H:35 , HOH H:6109 , DC K:21
BINDING SITE FOR RESIDUE NA H 6106
15
DC4
SOFTWARE
ASP I:35 , DC K:16
BINDING SITE FOR RESIDUE NA I 7107
16
DC5
SOFTWARE
ASP J:35 , DC L:24 , HOH L:36
BINDING SITE FOR RESIDUE NA J 8108
[
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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, 8)
Info
All PROSITE Patterns/Profiles
1: HTH_DTXR (G:4-65,H:4-65,I:4-65,J:4-65)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_DTXR
PS50944
DtxR-type HTH domain profile.
IDER_MYCTO
4-65
4
-
-
-
-
G:4-65
H:4-65
I:4-65
J:4-65
IDER_MYCTU
4-65
4
-
-
-
-
G:4-65
H:4-65
I:4-65
J:4-65
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1u8ra1 (A:1-64)
1b: SCOP_d1u8rb1 (B:1-64)
1c: SCOP_d1u8rc1 (C:1-64)
1d: SCOP_d1u8rd1 (D:1-64)
1e: SCOP_d1u8rg1 (G:1-64)
1f: SCOP_d1u8rh1 (H:1-64)
1g: SCOP_d1u8ri1 (I:1-64)
1h: SCOP_d1u8rj1 (J:1-64)
2a: SCOP_d1u8ra2 (A:65-141)
2b: SCOP_d1u8rb2 (B:65-141)
2c: SCOP_d1u8rc2 (C:65-141)
2d: SCOP_d1u8rd2 (D:65-141)
2e: SCOP_d1u8rg2 (G:65-141)
2f: SCOP_d1u8rh2 (H:65-141)
2g: SCOP_d1u8ri2 (I:65-141)
2h: SCOP_d1u8rj2 (J:65-141)
3a: SCOP_d1u8ra3 (A:151-230)
3b: SCOP_d1u8ri3 (I:151-230)
3c: SCOP_d1u8rj3 (J:150-230)
3d: SCOP_d1u8rb3 (B:151-230)
3e: SCOP_d1u8rc3 (C:151-230)
3f: SCOP_d1u8rd3 (D:151-230)
3g: SCOP_d1u8rg3 (G:151-230)
3h: SCOP_d1u8rh3 (H:150-230)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Winged helix DNA-binding domain
(576)
Family
:
Iron-dependent repressor protein
(44)
Protein domain
:
Iron-dependent regulator IdeR
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
1a
d1u8ra1
A:1-64
1b
d1u8rb1
B:1-64
1c
d1u8rc1
C:1-64
1d
d1u8rd1
D:1-64
1e
d1u8rg1
G:1-64
1f
d1u8rh1
H:1-64
1g
d1u8ri1
I:1-64
1h
d1u8rj1
J:1-64
Fold
:
Iron-dependent repressor protein, dimerization domain
(45)
Superfamily
:
Iron-dependent repressor protein, dimerization domain
(45)
Family
:
Iron-dependent repressor protein, dimerization domain
(44)
Protein domain
:
Iron-dependent regulator
(6)
Mycobacterium tuberculosis [TaxId: 1773]
(6)
2a
d1u8ra2
A:65-141
2b
d1u8rb2
B:65-141
2c
d1u8rc2
C:65-141
2d
d1u8rd2
D:65-141
2e
d1u8rg2
G:65-141
2f
d1u8rh2
H:65-141
2g
d1u8ri2
I:65-141
2h
d1u8rj2
J:65-141
Class
:
All beta proteins
(24004)
Fold
:
SH3-like barrel
(1035)
Superfamily
:
C-terminal domain of transcriptional repressors
(56)
Family
:
FeoA-like
(23)
Protein domain
:
Iron-dependent regulator IdeR
(2)
Mycobacterium tuberculosis [TaxId: 1773]
(2)
3a
d1u8ra3
A:151-230
3b
d1u8ri3
I:151-230
3c
d1u8rj3
J:150-230
3d
d1u8rb3
B:151-230
3e
d1u8rc3
C:151-230
3f
d1u8rd3
D:151-230
3g
d1u8rg3
G:151-230
3h
d1u8rh3
H:150-230
[
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]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1u8rA01 (A:1-73)
1b: CATH_1u8rB01 (B:1-73)
1c: CATH_1u8rC01 (C:1-73)
1d: CATH_1u8rD01 (D:1-73)
1e: CATH_1u8rG01 (G:1-73)
1f: CATH_1u8rH01 (H:1-73)
1g: CATH_1u8rI01 (I:1-73)
1h: CATH_1u8rJ01 (J:1-73)
2a: CATH_1u8rA02 (A:74-140)
2b: CATH_1u8rI02 (I:74-140)
2c: CATH_1u8rJ02 (J:74-140)
2d: CATH_1u8rB02 (B:74-140)
2e: CATH_1u8rC02 (C:74-140)
2f: CATH_1u8rD02 (D:74-140)
2g: CATH_1u8rG02 (G:74-140)
2h: CATH_1u8rH02 (H:74-140)
3a: CATH_1u8rA03 (A:151-230)
3b: CATH_1u8rB03 (B:151-230)
3c: CATH_1u8rC03 (C:151-230)
3d: CATH_1u8rD03 (D:151-230)
3e: CATH_1u8rG03 (G:151-230)
3f: CATH_1u8rH03 (H:151-230)
3g: CATH_1u8rI03 (I:151-230)
3h: CATH_1u8rJ03 (J:151-230)
View:
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)
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)
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(
)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
'winged helix' repressor DNA binding domain
(507)
[unclassified]
(77)
1a
1u8rA01
A:1-73
1b
1u8rB01
B:1-73
1c
1u8rC01
C:1-73
1d
1u8rD01
D:1-73
1e
1u8rG01
G:1-73
1f
1u8rH01
H:1-73
1g
1u8rI01
I:1-73
1h
1u8rJ01
J:1-73
Topology
:
Diphtheria Toxin Repressor; domain 2
(34)
Homologous Superfamily
:
Diphtheria Toxin Repressor, domain 2
(32)
[unclassified]
(5)
2a
1u8rA02
A:74-140
2b
1u8rI02
I:74-140
2c
1u8rJ02
J:74-140
2d
1u8rB02
B:74-140
2e
1u8rC02
C:74-140
2f
1u8rD02
D:74-140
2g
1u8rG02
G:74-140
2h
1u8rH02
H:74-140
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
SH3 type barrels.
(648)
Homologous Superfamily
:
[code=2.30.30.90, no name defined]
(14)
[unclassified]
(1)
3a
1u8rA03
A:151-230
3b
1u8rB03
B:151-230
3c
1u8rC03
C:151-230
3d
1u8rD03
D:151-230
3e
1u8rG03
G:151-230
3f
1u8rH03
H:151-230
3g
1u8rI03
I:151-230
3h
1u8rJ03
J:151-230
[
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]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_Fe_dep_repr_C_1u8rJ01 (J:65-135)
1b: PFAM_Fe_dep_repr_C_1u8rJ02 (J:65-135)
1c: PFAM_Fe_dep_repr_C_1u8rJ03 (J:65-135)
1d: PFAM_Fe_dep_repr_C_1u8rJ04 (J:65-135)
1e: PFAM_Fe_dep_repr_C_1u8rJ05 (J:65-135)
1f: PFAM_Fe_dep_repr_C_1u8rJ06 (J:65-135)
1g: PFAM_Fe_dep_repr_C_1u8rJ07 (J:65-135)
1h: PFAM_Fe_dep_repr_C_1u8rJ08 (J:65-135)
2a: PFAM_Fe_dep_repress_1u8rJ09 (J:3-62)
2b: PFAM_Fe_dep_repress_1u8rJ10 (J:3-62)
2c: PFAM_Fe_dep_repress_1u8rJ11 (J:3-62)
2d: PFAM_Fe_dep_repress_1u8rJ12 (J:3-62)
2e: PFAM_Fe_dep_repress_1u8rJ13 (J:3-62)
2f: PFAM_Fe_dep_repress_1u8rJ14 (J:3-62)
2g: PFAM_Fe_dep_repress_1u8rJ15 (J:3-62)
2h: PFAM_Fe_dep_repress_1u8rJ16 (J:3-62)
3a: PFAM_FeoA_1u8rJ17 (J:152-229)
3b: PFAM_FeoA_1u8rJ18 (J:152-229)
3c: PFAM_FeoA_1u8rJ19 (J:152-229)
3d: PFAM_FeoA_1u8rJ20 (J:152-229)
3e: PFAM_FeoA_1u8rJ21 (J:152-229)
3f: PFAM_FeoA_1u8rJ22 (J:152-229)
3g: PFAM_FeoA_1u8rJ23 (J:152-229)
3h: PFAM_FeoA_1u8rJ24 (J:152-229)
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Families
(
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(
)
Organisms
(
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(
)
Clan
:
HTH
(544)
Family
:
Fe_dep_repr_C
(11)
Mycobacterium tuberculosis
(1)
1a
Fe_dep_repr_C-1u8rJ01
J:65-135
1b
Fe_dep_repr_C-1u8rJ02
J:65-135
1c
Fe_dep_repr_C-1u8rJ03
J:65-135
1d
Fe_dep_repr_C-1u8rJ04
J:65-135
1e
Fe_dep_repr_C-1u8rJ05
J:65-135
1f
Fe_dep_repr_C-1u8rJ06
J:65-135
1g
Fe_dep_repr_C-1u8rJ07
J:65-135
1h
Fe_dep_repr_C-1u8rJ08
J:65-135
Family
:
Fe_dep_repress
(10)
Mycobacterium tuberculosis
(1)
2a
Fe_dep_repress-1u8rJ09
J:3-62
2b
Fe_dep_repress-1u8rJ10
J:3-62
2c
Fe_dep_repress-1u8rJ11
J:3-62
2d
Fe_dep_repress-1u8rJ12
J:3-62
2e
Fe_dep_repress-1u8rJ13
J:3-62
2f
Fe_dep_repress-1u8rJ14
J:3-62
2g
Fe_dep_repress-1u8rJ15
J:3-62
2h
Fe_dep_repress-1u8rJ16
J:3-62
Clan
:
TRB
(15)
Family
:
FeoA
(11)
Mycobacterium tuberculosis
(1)
3a
FeoA-1u8rJ17
J:152-229
3b
FeoA-1u8rJ18
J:152-229
3c
FeoA-1u8rJ19
J:152-229
3d
FeoA-1u8rJ20
J:152-229
3e
FeoA-1u8rJ21
J:152-229
3f
FeoA-1u8rJ22
J:152-229
3g
FeoA-1u8rJ23
J:152-229
3h
FeoA-1u8rJ24
J:152-229
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