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1O9R
Asym. Unit
Info
Asym.Unit (170 KB)
Biol.Unit 1 (328 KB)
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(1)
Title
:
THE X-RAY CRYSTAL STRUCTURE OF AGROBACTERIUM TUMEFACIENS DPS, A MEMBER OF THE FAMILY THAT PROTECT DNA WITHOUT BINDING
Authors
:
A. Ilari, P. Ceci, E. Chiancone
Date
:
18 Dec 02 (Deposition) - 29 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Iron-Binding Protein, Dna Protection From Oxidative Damage, Dna-Binding, Iron- Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Ceci, A. Ilari, E. Falvo, E. Chiancone
The Dps Protein Of Agrobacterium Tumefaciens Does Not Bind To Dna But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, And Hydroxyl-Radical Scavenging Properties
J. Biol. Chem. V. 278 20319 2003
(for further references see the
PDB file header
)
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
3a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
3b: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSb)
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Label:
No.
Name
Count
Type
Full Name
1
EDO
1
Ligand/Ion
1,2-ETHANEDIOL
2
FE
6
Ligand/Ion
FE (III) ION
3
TRS
2
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:67 , GLU A:71 , HIS B:40 , HOH B:2036 , HOH B:2045
BINDING SITE FOR RESIDUE FE A1163
2
AC2
SOFTWARE
HIS A:40 , HOH A:2041 , HOH A:2046 , ASP B:67 , GLU B:71
BINDING SITE FOR RESIDUE FE B1163
3
AC3
SOFTWARE
HIS C:40 , ASP C:67 , GLU C:71 , HOH C:2032 , HOH C:2037
BINDING SITE FOR RESIDUE FE C1163
4
AC4
SOFTWARE
HIS D:40 , ASP D:67 , GLU D:71 , HOH D:2036 , HOH D:2048
BINDING SITE FOR RESIDUE FE D1163
5
AC5
SOFTWARE
ASP E:67 , GLU E:71 , HOH E:2050 , HIS F:40 , HOH F:2034 , HOH F:2043
BINDING SITE FOR RESIDUE FE E1163
6
AC6
SOFTWARE
HIS E:40 , HOH E:2028 , HOH E:2035 , ASP F:67 , GLU F:71 , HOH F:2057
BINDING SITE FOR RESIDUE FE F1163
7
AC7
SOFTWARE
ASP B:138 , HOH B:2132 , HOH B:2133 , HOH B:2134 , ASP D:138 , ASP F:138 , ARG F:145
BINDING SITE FOR RESIDUE TRS B1164
8
AC8
SOFTWARE
ILE D:30 , ARG D:59 , ASP D:63 , ASP D:67 , HOH D:2115
BINDING SITE FOR RESIDUE EDO D1164
9
AC9
SOFTWARE
ASP A:138 , ASP C:138 , ASP E:138 , HOH E:2114 , HOH E:2115 , HOH E:2116
BINDING SITE FOR RESIDUE TRS E1164
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: DPS_1 (A:40-56,B:40-56,C:40-56,D:40-56,E:...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DPS_1
PS00818
Dps protein family signature 1.
DPS_AGRFC
40-56
6
A:40-56
B:40-56
C:40-56
D:40-56
E:40-56
F:40-56
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Exons
(0, 0)
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1o9ra_ (A:)
1b: SCOP_d1o9rb_ (B:)
1c: SCOP_d1o9rc_ (C:)
1d: SCOP_d1o9rd_ (D:)
1e: SCOP_d1o9re_ (E:)
1f: SCOP_d1o9rf_ (F:)
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Protein Domains
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Organisms
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Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Dodecameric ferritin homolog
(44)
Agrobacterium tumefaciens, Dps [TaxId: 358]
(1)
1a
d1o9ra_
A:
1b
d1o9rb_
B:
1c
d1o9rc_
C:
1d
d1o9rd_
D:
1e
d1o9re_
E:
1f
d1o9rf_
F:
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1o9rA00 (A:1-162)
1b: CATH_1o9rB00 (B:1-162)
1c: CATH_1o9rE00 (E:1-162)
1d: CATH_1o9rF00 (F:1-162)
1e: CATH_1o9rD00 (D:3-162)
1f: CATH_1o9rC00 (C:4-162)
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Organisms
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Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Agrobacterium tumefaciens. Organism_taxid: 358. Strain: gv3101.
(1)
1a
1o9rA00
A:1-162
1b
1o9rB00
B:1-162
1c
1o9rE00
E:1-162
1d
1o9rF00
F:1-162
1e
1o9rD00
D:3-162
1f
1o9rC00
C:4-162
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (170 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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