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2O3F
Asym. Unit
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Asym.Unit (53 KB)
Biol.Unit 1 (17 KB)
Biol.Unit 2 (17 KB)
Biol.Unit 3 (17 KB)
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(1)
Title
:
STRUCTURAL GENOMICS, THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE PUTATIVE TRANSCRIPTIONAL REGULATOR YBBH FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168.
Authors
:
K. Tan, L. Bigelow, J. Abdullah, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date
:
01 Dec 06 (Deposition) - 02 Jan 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Apc85504, Putative Transcriptional Regulator Ybbh, Bacillus Subtilis Subsp. Subtilis Str. 168, Structural Genomics, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Tan, L. Bigelow, J. Abdullah, A. Joachimiak
The Crystal Structure Of The N-Terminal Domain Of The Putative Transcriptional Regulator Ybbh From Bacillus Subtilis Subsp. Subtilis Str. 168.
To Be Published
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 38)
Info
All Hetero Components
1a: N-DIMETHYL-LYSINE (MLYa)
1b: N-DIMETHYL-LYSINE (MLYb)
1c: N-DIMETHYL-LYSINE (MLYc)
1d: N-DIMETHYL-LYSINE (MLYd)
1e: N-DIMETHYL-LYSINE (MLYe)
1f: N-DIMETHYL-LYSINE (MLYf)
1g: N-DIMETHYL-LYSINE (MLYg)
1h: N-DIMETHYL-LYSINE (MLYh)
1i: N-DIMETHYL-LYSINE (MLYi)
1j: N-DIMETHYL-LYSINE (MLYj)
1k: N-DIMETHYL-LYSINE (MLYk)
1l: N-DIMETHYL-LYSINE (MLYl)
1m: N-DIMETHYL-LYSINE (MLYm)
1n: N-DIMETHYL-LYSINE (MLYn)
1o: N-DIMETHYL-LYSINE (MLYo)
2a: SELENOMETHIONINE (MSEa)
2b: SELENOMETHIONINE (MSEb)
2c: SELENOMETHIONINE (MSEc)
2d: SELENOMETHIONINE (MSEd)
2e: SELENOMETHIONINE (MSEe)
2f: SELENOMETHIONINE (MSEf)
2g: SELENOMETHIONINE (MSEg)
2h: SELENOMETHIONINE (MSEh)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
3h: SULFATE ION (SO4h)
3i: SULFATE ION (SO4i)
3j: SULFATE ION (SO4j)
3k: SULFATE ION (SO4k)
3l: SULFATE ION (SO4l)
3m: SULFATE ION (SO4m)
3n: SULFATE ION (SO4n)
3o: SULFATE ION (SO4o)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MLY
15
Mod. Amino Acid
N-DIMETHYL-LYSINE
2
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
3
SO4
15
Ligand/Ion
SULFATE ION
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA C:29 , HIS C:30 , PRO C:31 , HIS C:32 , MLY C:33
BINDING SITE FOR RESIDUE SO4 C 201
02
AC2
SOFTWARE
HIS B:30 , PRO B:31 , HIS B:32 , MLY B:33 , HOH B:228 , HOH B:247 , MLY C:15
BINDING SITE FOR RESIDUE SO4 B 202
03
AC3
SOFTWARE
ALA A:29 , HIS A:30 , PRO A:31 , HIS A:32 , MLY A:33 , MLY B:15
BINDING SITE FOR RESIDUE SO4 A 203
04
AC4
SOFTWARE
SER B:49 , ARG B:55 , HOH B:244 , HOH B:249
BINDING SITE FOR RESIDUE SO4 B 204
05
AC5
SOFTWARE
SER C:49 , ALA C:51 , ALA C:52 , ARG C:55 , SO4 C:212 , HOH C:244 , HOH C:256
BINDING SITE FOR RESIDUE SO4 C 205
06
AC6
SOFTWARE
SER A:49 , ALA A:51 , ALA A:52 , ARG A:55 , HOH A:256
BINDING SITE FOR RESIDUE SO4 A 206
07
AC7
SOFTWARE
GLN B:10 , MLY B:13 , HIS B:14
BINDING SITE FOR RESIDUE SO4 B 207
08
AC8
SOFTWARE
GLN C:10 , MLY C:13 , HIS C:14
BINDING SITE FOR RESIDUE SO4 C 208
09
AC9
SOFTWARE
GLN A:10 , MLY A:13 , HIS A:14
BINDING SITE FOR RESIDUE SO4 A 209
10
BC1
SOFTWARE
PRO A:17 , PRO A:18 , SER A:19 , GLU A:20 , ARG A:55
BINDING SITE FOR RESIDUE SO4 A 210
11
BC2
SOFTWARE
PRO B:17 , PRO B:18 , SER B:19 , GLU B:20 , ARG B:55
BINDING SITE FOR RESIDUE SO4 B 211
12
BC3
SOFTWARE
PRO C:17 , PRO C:18 , SER C:19 , GLU C:20 , ARG C:55 , SO4 C:205
BINDING SITE FOR RESIDUE SO4 C 212
13
BC4
SOFTWARE
ILE C:54 , GLY C:64 , PHE C:65 , GLN C:66 , HOH C:225 , HOH C:240
BINDING SITE FOR RESIDUE SO4 C 213
14
BC5
SOFTWARE
GLY A:64 , PHE A:65 , GLN A:66 , HOH A:220 , HOH A:221
BINDING SITE FOR RESIDUE SO4 A 214
15
BC6
SOFTWARE
GLY B:64 , PHE B:65 , GLN B:66 , HOH B:238 , HOH B:250
BINDING SITE FOR RESIDUE SO4 B 215
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: HTH_RPIR (A:3-79,B:3-79,C:3-79)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HTH_RPIR
PS51071
RpiR-type HTH domain profile.
YBBH_BACSU
3-79
3
A:3-79
B:3-79
C:3-79
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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
(1, 3)
Info
All SCOP Domains
1a: SCOP_d2o3fa1 (A:1-83)
1b: SCOP_d2o3fb_ (B:)
1c: SCOP_d2o3fc_ (C:)
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Protein Domains
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(
)
Organisms
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
DNA/RNA-binding 3-helical bundle
(1299)
Superfamily
:
Homeodomain-like
(373)
Family
:
RpiR-like
(1)
Protein domain
:
Putative transcriptional regulator YbbH
(1)
Bacillus subtilis [TaxId: 1423]
(1)
1a
d2o3fa1
A:1-83
1b
d2o3fb_
B:
1c
d2o3fc_
C:
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_2o3fA00 (A:2-83)
1b: CATH_2o3fB00 (B:2-83)
1c: CATH_2o3fC00 (C:2-83)
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)
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)
Bacillus subtilis. Organism_taxid: 1423. Strain: 168. Variant: bacillus subtilis subsp. Subtilis.
(1)
1a
2o3fA00
A:2-83
1b
2o3fB00
B:2-83
1c
2o3fC00
C:2-83
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_HTH_6_2o3fC01 (C:3-79)
1b: PFAM_HTH_6_2o3fC02 (C:3-79)
1c: PFAM_HTH_6_2o3fC03 (C:3-79)
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Clan
:
HTH
(544)
Family
:
HTH_6
(1)
Bacillus subtilis
(1)
1a
HTH_6-2o3fC01
C:3-79
1b
HTH_6-2o3fC02
C:3-79
1c
HTH_6-2o3fC03
C:3-79
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