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3L5O
Biol. Unit 3
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Asym.Unit (90 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (43 KB)
Biol.Unit 3 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PROTEIN WITH UNKNOWN FUNCTION FROM DUF364 FAMILY (ZP_00559375.1) FROM DESULFITOBACTERIUM HAFNIENSE DCB-2 AT 2.01 A RESOLUTION
Authors
:
Joint Center For Structural Genomics, Joint Center For Struct Genomics (Jcsg)
Date
:
22 Dec 09 (Deposition) - 02 Feb 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.01
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Rare Metals, Siderophores, Adenosyl Binding Site, Protein With Unknown Function From Duf364 Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Adenosyl Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
M. D. Miller, L. Aravind, C. Bakolitsa, C. L. Rife, D. Carlton, P. Abdubek, T. Astakhova, H. L. Axelrod, H. J. Chiu, T. Clayton, M. C. Deller, L. Duan, J. Feuerhelm, J. C. Grant, G. W. Han, L. Jaroszewski, K. K. Jin, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, A. Kumar, D. Marciano, D. Mcmullan, A. T. Morse, E. Nigoghossian, L. Okach, R. Reyes, H. Van Den Bedem, D. Weekes, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structure Of The First Representative Of Pfam Family Pf0401 (Duf364) Reveals Enolase And Rossmann-Like Folds That Combine To Form A Unique Active Site With A Possible Role I Heavy-Metal Chelation.
Acta Crystallogr. , Sect. F V. 66 1167 2010
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Hetero Components
(3, 22)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
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)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
3c: IMIDAZOLE (IMDc)
3d: IMIDAZOLE (IMDd)
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)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
IMD
4
Ligand/Ion
IMIDAZOLE
4
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
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Sites
(12, 12)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:148 , TRP A:149 , IMD A:303 , HOH A:372 , HOH A:445
BINDING SITE FOR RESIDUE CL A 301
02
AC2
SOFTWARE
TRP A:149 , LEU A:158 , THR A:174 , SER A:177 , ASP A:180 , THR A:182 , CL A:301 , HOH A:445
BINDING SITE FOR RESIDUE IMD A 303
03
AC3
SOFTWARE
PRO A:40 , ARG A:42 , TYR A:72 , ALA A:176 , ASP A:180 , HOH A:482
BINDING SITE FOR RESIDUE IMD A 304
04
AC4
SOFTWARE
GLY A:200 , SER A:218 , GLY A:219 , TYR A:241 , LYS A:246 , EDO A:311
BINDING SITE FOR RESIDUE EDO A 307
05
AC5
SOFTWARE
ASP A:111 , PRO A:112 , LYS A:246 , EDO A:307 , HOH A:489
BINDING SITE FOR RESIDUE EDO A 311
06
AC6
SOFTWARE
GLU B:148 , TRP B:149 , IMD B:302 , EDO B:310 , HOH B:477
BINDING SITE FOR RESIDUE CL B 301
07
AC7
SOFTWARE
VAL B:128 , LEU B:158 , ALA B:176 , SER B:177 , ASP B:180 , THR B:182 , CL B:301 , HOH B:477
BINDING SITE FOR RESIDUE IMD B 302
08
AC8
SOFTWARE
PRO B:40 , ARG B:42 , GLU B:45 , TYR B:72 , ALA B:176
BINDING SITE FOR RESIDUE IMD B 305
09
AC9
SOFTWARE
GLU B:20 , ARG B:31 , ASN B:225 , ALA B:226 , PHE B:229
BINDING SITE FOR RESIDUE EDO B 306
10
BC1
SOFTWARE
GLN B:-1 , PHE B:-2 , MSE B:1 , TRP B:2
BINDING SITE FOR RESIDUE EDO B 308
11
BC2
SOFTWARE
ASP B:15 , GLY B:154 , TYR B:156
BINDING SITE FOR RESIDUE EDO B 309
12
BC3
SOFTWARE
GLY B:129 , HIS B:130 , THR B:174 , CL B:301
BINDING SITE FOR RESIDUE EDO B 310
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3l5oa_ (A:)
1b: SCOP_d3l5ob_ (B:)
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Protein Domains
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Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PLP-dependent transferase-like
(627)
Superfamily
:
Dhaf3308-like
(1)
Family
:
Dhaf3308-like
(1)
Protein domain
:
Hypothetical protein Dhaf_3308
(1)
Desulfitobacterium hafniense [TaxId: 49338]
(1)
1a
d3l5oa_
A:
1b
d3l5ob_
B:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_DUF364_3l5oB01 (B:115-251)
1b: PFAM_DUF364_3l5oB02 (B:115-251)
2a: PFAM_DUF4213_3l5oB03 (B:4-87)
2b: PFAM_DUF4213_3l5oB04 (B:4-87)
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Clan
:
no clan defined [family: DUF364]
(2)
Family
:
DUF364
(2)
Desulfitobacterium hafniense (strain DCB-2 / DSM 10664)
(1)
1a
DUF364-3l5oB01
B:115-251
1b
DUF364-3l5oB02
B:115-251
Clan
:
no clan defined [family: DUF4213]
(2)
Family
:
DUF4213
(2)
Desulfitobacterium hafniense (strain DCB-2 / DSM 10664)
(1)
2a
DUF4213-3l5oB03
B:4-87
2b
DUF4213-3l5oB04
B:4-87
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Asym.Unit (90 KB)
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