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Asym. Unit
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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
[
close entry info
]
Hetero Components
(4, 58)
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
17
Ligand/Ion
1,2-ETHANEDIOL
3
FMT
24
Ligand/Ion
FORMIC ACID
4
MSE
16
Mod. Amino Acid
SELENOMETHIONINE
[
close Hetero Component info
]
Sites
(38, 38)
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)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: 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
AC2
SOFTWARE
ALA A:111 , THR A:126 , TYR A:128 , HOH A:320
BINDING SITE FOR RESIDUE EDO A 174
03
AC3
SOFTWARE
ILE A:132 , GLU A:133 , ASP B:4 , VAL B:8 , HOH B:188
BINDING SITE FOR RESIDUE EDO A 175
04
AC4
SOFTWARE
LEU A:5 , GLN A:9 , PHE A:10 , ILE A:136 , TYR A:140 , ILE B:132 , ILE B:136
BINDING SITE FOR RESIDUE EDO A 176
05
AC5
SOFTWARE
ASN A:18 , ASP A:22 , ARG A:89 , HOH A:199 , HOH A:256
BINDING SITE FOR RESIDUE EDO A 177
06
AC6
SOFTWARE
GLY B:0 , ASP B:4 , HOH B:270
BINDING SITE FOR RESIDUE EDO B 174
07
AC7
SOFTWARE
ILE A:132 , ILE A:136 , PRO A:137 , LEU B:5 , GLN B:9 , PHE B:10 , TYR B:140
BINDING SITE FOR RESIDUE EDO B 175
08
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
09
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
10
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
11
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
12
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
13
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
14
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
15
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
16
BC7
SOFTWARE
GLN D:71 , TYR D:98 , GLY D:101
BINDING SITE FOR RESIDUE EDO D 177
17
BC8
SOFTWARE
SER D:41 , ARG D:42 , HIS D:152 , ASN D:153 , HOH D:216
BINDING SITE FOR RESIDUE EDO D 178
18
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
19
CC1
SOFTWARE
ASN A:40 , ARG A:42 , HOH A:235 , VAL D:37
BINDING SITE FOR RESIDUE FMT A 178
20
CC2
SOFTWARE
GLN A:71 , PHE A:102 , ASP A:106 , HOH A:248
BINDING SITE FOR RESIDUE FMT A 179
21
CC3
SOFTWARE
ASP A:4 , HOH A:193
BINDING SITE FOR RESIDUE FMT A 181
22
CC4
SOFTWARE
ASP A:36 , ASN A:40 , HOH A:196 , HOH A:332 , HOH D:201
BINDING SITE FOR RESIDUE FMT A 182
23
CC5
SOFTWARE
GLN A:71 , THR A:74 , ALA A:75 , TYR A:98
BINDING SITE FOR RESIDUE FMT A 183
24
CC6
SOFTWARE
ASP A:59 , HOH A:267
BINDING SITE FOR RESIDUE FMT A 184
25
CC7
SOFTWARE
LYS A:12 , ASN A:16 , GLY A:164 , ALA A:165 , HOH A:259 , HOH A:276
BINDING SITE FOR RESIDUE FMT A 185
26
CC8
SOFTWARE
ALA A:108 , ALA A:111
BINDING SITE FOR RESIDUE FMT A 186
27
CC9
SOFTWARE
GLN A:47 , TYR B:147 , ARG B:151 , FMT B:185 , HOH B:201
BINDING SITE FOR RESIDUE FMT B 180
28
DC1
SOFTWARE
LYS B:23 , PHE B:27 , VAL B:155 , GLU B:156
BINDING SITE FOR RESIDUE FMT B 182
29
DC2
SOFTWARE
LYS B:12 , ASN B:16 , GLY B:164 , ALA B:165
BINDING SITE FOR RESIDUE FMT B 183
30
DC3
SOFTWARE
THR B:84
BINDING SITE FOR RESIDUE FMT B 184
31
DC4
SOFTWARE
PHE A:48 , PHE A:141 , HIS A:142 , LYS B:159 , FMT B:180 , HOH B:189
BINDING SITE FOR RESIDUE FMT B 185
32
DC5
SOFTWARE
LYS C:23 , ASP C:161
BINDING SITE FOR RESIDUE FMT C 176
33
DC6
SOFTWARE
GLU C:133 , HOH D:192
BINDING SITE FOR RESIDUE FMT C 177
34
DC7
SOFTWARE
GLN C:71 , GLY C:101 , HOH C:230
BINDING SITE FOR RESIDUE FMT C 179
35
DC8
SOFTWARE
LYS C:23 , PHE C:27 , VAL C:155 , GLU C:156
BINDING SITE FOR RESIDUE FMT C 180
36
DC9
SOFTWARE
ASP A:4 , GLU A:104
BINDING SITE FOR RESIDUE FMT D 181
37
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
38
EC2
SOFTWARE
ALA D:111 , THR D:126
BINDING SITE FOR RESIDUE FMT D 183
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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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, 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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Protein Domains
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)
(
)
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:
[
close SCOP info
]
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
[
close CATH info
]
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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