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Biol. Unit 2
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Asym.Unit (139 KB)
Biol.Unit 1 (68 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A DINB FAMILY MEMBER PROTEIN (SDEN_0562) FROM SHEWANELLA DENITRIFICANS AT 1.83 A RESOLUTION
Authors
:
Joint Center For Structural Genomics (Jcsg)
Date
:
31 Jan 07 (Deposition) - 13 Feb 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.83
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Yp_561575. 1) Fro Shewanella Denitrificans Os-217 At 1. 83 A Resolution
To Be Published
[
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
3a: FORMIC ACID (FMTa)
3b: FORMIC ACID (FMTb)
3c: FORMIC ACID (FMTc)
3d: FORMIC ACID (FMTd)
3e: FORMIC ACID (FMTe)
3f: FORMIC ACID (FMTf)
3g: FORMIC ACID (FMTg)
3h: FORMIC ACID (FMTh)
3i: FORMIC ACID (FMTi)
3j: FORMIC ACID (FMTj)
3k: FORMIC ACID (FMTk)
3l: FORMIC ACID (FMTl)
3m: FORMIC ACID (FMTm)
3n: FORMIC ACID (FMTn)
3o: FORMIC ACID (FMTo)
3p: FORMIC ACID (FMTp)
3q: FORMIC ACID (FMTq)
3r: FORMIC ACID (FMTr)
3s: FORMIC ACID (FMTs)
3t: FORMIC ACID (FMTt)
3u: FORMIC ACID (FMTu)
3v: FORMIC ACID (FMTv)
3w: FORMIC ACID (FMTw)
3x: FORMIC ACID (FMTx)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
3
FMT
9
Ligand/Ion
FORMIC ACID
4
MSE
8
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC1 (SOFTWARE)
05: BC2 (SOFTWARE)
06: BC3 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC7 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC4 (SOFTWARE)
15: DC5 (SOFTWARE)
16: DC6 (SOFTWARE)
17: DC7 (SOFTWARE)
18: DC8 (SOFTWARE)
19: EC1 (SOFTWARE)
20: EC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG D:42 , ASN D:49 , EDO D:179
BINDING SITE FOR RESIDUE CL D 174
02
AC8
SOFTWARE
HIS A:152 , LEU B:43 , ALA B:44 , HOH B:191 , HOH B:196 , HIS C:152 , ASN C:153 , HOH C:185
BINDING SITE FOR RESIDUE EDO B 176
03
AC9
SOFTWARE
ASN B:153 , GLY B:154 , HOH B:248 , ALA C:44 , ALA C:45 , ARG D:151 , HIS D:152 , GLY D:154 , EDO D:175
BINDING SITE FOR RESIDUE EDO B 177
04
BC1
SOFTWARE
VAL B:37 , ASN B:40 , SER B:41 , EDO B:179 , HOH B:235 , ASN C:40 , ARG C:42
BINDING SITE FOR RESIDUE EDO B 178
05
BC2
SOFTWARE
SER B:41 , ARG B:42 , HIS B:152 , ASN B:153 , EDO B:178 , HOH C:207
BINDING SITE FOR RESIDUE EDO B 179
06
BC3
SOFTWARE
HIS A:152 , ASN A:153 , HOH A:198 , HIS C:152 , HOH C:183 , HOH C:186 , HOH C:240 , LEU D:43 , ALA D:44
BINDING SITE FOR RESIDUE EDO C 174
07
BC4
SOFTWARE
LEU C:5 , GLN C:9 , PHE C:10 , ILE C:136 , TYR C:140 , ILE D:132 , ILE D:136
BINDING SITE FOR RESIDUE EDO C 175
08
BC5
SOFTWARE
ALA A:44 , ALA A:45 , ARG B:151 , HIS B:152 , GLY B:154 , EDO B:177 , ASN D:153 , HOH D:277
BINDING SITE FOR RESIDUE EDO D 175
09
BC6
SOFTWARE
ILE C:132 , ILE C:136 , LEU D:5 , GLN D:9 , PHE D:10 , TYR D:140
BINDING SITE FOR RESIDUE EDO D 176
10
BC7
SOFTWARE
GLN D:71 , TYR D:98 , GLY D:101
BINDING SITE FOR RESIDUE EDO D 177
11
BC8
SOFTWARE
SER D:41 , ARG D:42 , HIS D:152 , ASN D:153 , HOH D:216
BINDING SITE FOR RESIDUE EDO D 178
12
BC9
SOFTWARE
VAL A:37 , ARG D:42 , PHE D:48 , CL D:174 , HOH D:217 , HOH D:231
BINDING SITE FOR RESIDUE EDO D 179
13
CC1
SOFTWARE
ASN A:40 , ARG A:42 , HOH A:235 , VAL D:37
BINDING SITE FOR RESIDUE FMT A 178
14
CC4
SOFTWARE
ASP A:36 , ASN A:40 , HOH A:196 , HOH A:332 , HOH D:201
BINDING SITE FOR RESIDUE FMT A 182
15
DC5
SOFTWARE
LYS C:23 , ASP C:161
BINDING SITE FOR RESIDUE FMT C 176
16
DC6
SOFTWARE
GLU C:133 , HOH D:192
BINDING SITE FOR RESIDUE FMT C 177
17
DC7
SOFTWARE
GLN C:71 , GLY C:101 , HOH C:230
BINDING SITE FOR RESIDUE FMT C 179
18
DC8
SOFTWARE
LYS C:23 , PHE C:27 , VAL C:155 , GLU C:156
BINDING SITE FOR RESIDUE FMT C 180
19
EC1
SOFTWARE
LYS B:31 , ASP C:46 , HOH C:219 , ARG D:151 , GLY D:154 , VAL D:155
BINDING SITE FOR RESIDUE FMT D 182
20
EC2
SOFTWARE
ALA D:111 , THR D:126
BINDING SITE FOR RESIDUE FMT D 183
[
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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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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2oqma1 (A:1-171)
1b: SCOP_d2oqmb_ (B:)
1c: SCOP_d2oqmc_ (C:)
1d: SCOP_d2oqmd_ (D:)
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(
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
DinB/YfiT-like putative metalloenzymes
(8)
Superfamily
:
DinB/YfiT-like putative metalloenzymes
(8)
Family
:
Sden0562-like
(1)
Protein domain
:
Hypothetical protein Sden0562
(1)
Shewanella denitrificans [TaxId: 192073]
(1)
1a
d2oqma1
A:1-171
1b
d2oqmb_
B:
1c
d2oqmc_
C:
1d
d2oqmd_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2oqmB01 (B:-4-164)
1b: CATH_2oqmC01 (C:-5-164)
1c: CATH_2oqmD01 (D:-6-164)
1d: CATH_2oqmA01 (A:-8-164)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
dinb family like domain
(9)
Shewanella denitrificans. Organism_taxid: 192073. Strain: os217, dsm 15013.
(1)
1a
2oqmB01
B:-4-164
1b
2oqmC01
C:-5-164
1c
2oqmD01
D:-6-164
1d
2oqmA01
A:-8-164
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_DUF1993_2oqmD01 (D:2-164)
1b: PFAM_DUF1993_2oqmD02 (D:2-164)
1c: PFAM_DUF1993_2oqmD03 (D:2-164)
1d: PFAM_DUF1993_2oqmD04 (D:2-164)
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Clan
:
DinB
(11)
Family
:
DUF1993
(2)
Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013)
(1)
1a
DUF1993-2oqmD01
D:2-164
1b
DUF1993-2oqmD02
D:2-164
1c
DUF1993-2oqmD03
D:2-164
1d
DUF1993-2oqmD04
D:2-164
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Asymmetric Unit 1
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