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Biol. Unit 1
Info
Asym.Unit (226 KB)
Biol.Unit 1 (641 KB)
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(1)
Title
:
OXIDIZED (ALL FERRIC) FORM OF THE AZOTOBACTER VINELANDII BACTERIOFERRITIN
Authors
:
L. Swartz, K. Kunchinskas, H. Li, T. L. Poulos, W. N. Lanzilotta
Date
:
05 Jan 06 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (3x)
Keywords
:
Bacterioferritin, Ferritin, Diiron Site, Iron Transport, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Swartz, M. Kuchinskas, H. Li, T. L. Poulos, W. N. Lanzilotta
Redox-Dependent Structural Changes In The Azotobacter Vinelandii Bacterioferritin: New Insights Into The Ferroxidase And Iron Transport Mechanism(, ).
Biochemistry V. 45 4421 2006
[
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Hetero Components
(2, 66)
Info
All Hetero Components
1a: FE (II) ION (FE2a)
1b: FE (II) ION (FE2b)
1c: FE (II) ION (FE2c)
1d: FE (II) ION (FE2d)
1e: FE (II) ION (FE2e)
1f: FE (II) ION (FE2f)
1g: FE (II) ION (FE2g)
1h: FE (II) ION (FE2h)
1i: FE (II) ION (FE2i)
1j: FE (II) ION (FE2j)
1k: FE (II) ION (FE2k)
1l: FE (II) ION (FE2l)
1m: FE (II) ION (FE2m)
1n: FE (II) ION (FE2n)
1o: FE (II) ION (FE2o)
1p: FE (II) ION (FE2p)
1q: FE (II) ION (FE2q)
1r: FE (II) ION (FE2r)
2a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
2b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
2c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
2d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE2
54
Ligand/Ion
FE (II) ION
2
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(34, 34)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:18 , GLU A:51 , HIS A:54 , GLU A:127 , FE2 A:1602
BINDING SITE FOR RESIDUE FE2 A 1601
02
AC2
SOFTWARE
GLU A:51 , GLU A:94 , GLU A:127 , HIS A:130 , FE2 A:1601
BINDING SITE FOR RESIDUE FE2 A 1602
03
AC3
SOFTWARE
ASN A:148 , GLN A:151 , ASN F:148 , GLN F:151 , ASN G:148 , GLN G:151 , HOH G:3007 , ASN H:148 , GLN H:151
BINDING SITE FOR RESIDUE FE2 A 1603
04
AC4
SOFTWARE
GLU B:51 , GLU B:94 , GLU B:127 , HIS B:130 , FE2 B:1606
BINDING SITE FOR RESIDUE FE2 B 1605
05
AC5
SOFTWARE
GLU B:18 , GLU B:51 , HIS B:54 , GLU B:127 , FE2 B:1605
BINDING SITE FOR RESIDUE FE2 B 1606
06
AC6
SOFTWARE
ASN B:148 , GLN B:151 , ASN C:148 , GLN C:151 , ASN D:148 , GLN D:151 , HOH D:1742 , ASN E:148 , GLN E:151
BINDING SITE FOR RESIDUE FE2 B 1607
07
AC7
SOFTWARE
GLU C:18 , GLU C:51 , HIS C:54 , GLU C:127 , FE2 C:1610
BINDING SITE FOR RESIDUE FE2 C 1608
08
AC8
SOFTWARE
GLU C:51 , GLU C:94 , GLU C:127 , HIS C:130 , FE2 C:1608
BINDING SITE FOR RESIDUE FE2 C 1610
09
AC9
SOFTWARE
GLU D:18 , GLU D:51 , HIS D:54 , GLU D:127 , FE2 D:1612
BINDING SITE FOR RESIDUE FE2 D 1611
10
BC1
SOFTWARE
GLU D:51 , GLU D:94 , GLU D:127 , HIS D:130 , FE2 D:1611
BINDING SITE FOR RESIDUE FE2 D 1612
11
BC2
SOFTWARE
GLU E:18 , GLU E:51 , HIS E:54 , GLU E:127 , FE2 E:1614
BINDING SITE FOR RESIDUE FE2 E 1613
12
BC3
SOFTWARE
GLU E:51 , GLU E:94 , GLU E:127 , HIS E:130 , FE2 E:1613
BINDING SITE FOR RESIDUE FE2 E 1614
13
BC4
SOFTWARE
GLU F:18 , GLU F:51 , HIS F:54 , GLU F:127 , FE2 F:1617
BINDING SITE FOR RESIDUE FE2 F 1616
14
BC5
SOFTWARE
GLU F:51 , GLU F:94 , GLU F:127 , HIS F:130 , FE2 F:1616
BINDING SITE FOR RESIDUE FE2 F 1617
15
BC6
SOFTWARE
GLU G:18 , GLU G:51 , HIS G:54 , GLU G:127 , FE2 G:1619
BINDING SITE FOR RESIDUE FE2 G 1618
16
BC7
SOFTWARE
GLU G:51 , GLU G:94 , GLU G:127 , HIS G:130 , FE2 G:1618
BINDING SITE FOR RESIDUE FE2 G 1619
17
BC8
SOFTWARE
GLU H:18 , GLU H:51 , HIS H:54 , GLU H:127 , FE2 H:1622
BINDING SITE FOR RESIDUE FE2 H 1621
18
BC9
SOFTWARE
GLU H:51 , GLU H:94 , GLU H:127 , HIS H:130 , FE2 H:1621
BINDING SITE FOR RESIDUE FE2 H 1622
19
CC1
SOFTWARE
HOH B:1719
BINDING SITE FOR RESIDUE MG A 1701
20
CC2
SOFTWARE
HOH A:3013
BINDING SITE FOR RESIDUE MG B 1702
21
CC3
SOFTWARE
GLU A:135
BINDING SITE FOR RESIDUE MG A 1703
22
CC4
SOFTWARE
GLU D:85 , HOH D:1713 , GLU H:81 , GLU H:85 , HOH H:1756 , HOH H:1757
BINDING SITE FOR RESIDUE MG D 1705
23
CC5
SOFTWARE
HOH E:3022
BINDING SITE FOR RESIDUE MG C 1706
24
CC6
SOFTWARE
ASP C:34 , HOH C:3057 , HOH C:3058 , ASP D:132 , HOH D:1761 , HOH D:1762
BINDING SITE FOR RESIDUE MG D 1707
25
CC7
SOFTWARE
HOH E:3051 , HOH E:3052
BINDING SITE FOR RESIDUE MG G 1708
26
CC8
SOFTWARE
HOH H:1728 , HOH H:1742 , HOH H:1770
BINDING SITE FOR RESIDUE MG G 1709
27
CC9
SOFTWARE
GLU A:118 , HOH A:3031 , GLU E:118 , HOH E:3047 , GLU G:118 , GLU G:121
BINDING SITE FOR RESIDUE MG A 1710
28
DC1
SOFTWARE
GLU B:118 , GLU C:118 , GLU C:121 , HOH C:3042 , GLU F:118 , GLU F:121 , HOH F:1735
BINDING SITE FOR RESIDUE MG F 1711
29
DC2
SOFTWARE
GLU D:118 , GLU D:121 , HOH D:1741 , HOH D:1759
BINDING SITE FOR RESIDUE MG D 1712
30
DC3
SOFTWARE
GLU H:118 , GLU H:121 , HOH H:1765 , HOH H:1766
BINDING SITE FOR RESIDUE MG H 1713
31
DC4
SOFTWARE
LEU A:19 , ILE A:22 , ASN A:23 , PHE A:26 , TYR A:45 , ILE A:49 , MET A:52 , LEU B:19 , ILE B:22 , ASN B:23 , PHE B:26 , TYR B:45 , ILE B:49 , MET B:52 , LYS B:53
BINDING SITE FOR RESIDUE HEM A 3001
32
DC5
SOFTWARE
ASN C:23 , PHE C:26 , TYR C:45 , MET C:52 , LYS C:53 , ILE C:59 , HOH C:3055 , ILE D:22 , ASN D:23 , PHE D:26 , TYR D:45 , ILE D:49 , MET D:52 , LYS D:53
BINDING SITE FOR RESIDUE HEM C 3002
33
DC6
SOFTWARE
LEU E:19 , ILE E:22 , PHE E:26 , TYR E:45 , MET E:52 , LYS E:53 , LEU E:71 , LEU F:19 , ILE F:22 , PHE F:26 , TYR F:45 , ILE F:49 , MET F:52 , LYS F:53
BINDING SITE FOR RESIDUE HEM E 3003
34
DC7
SOFTWARE
LEU G:19 , ASN G:23 , PHE G:26 , TYR G:45 , ILE G:49 , MET G:52 , HOH G:3069 , ASN H:23 , PHE H:26 , TYR H:45 , MET H:52 , LYS H:53
BINDING SITE FOR RESIDUE HEM G 3004
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 48)
Info
All PROSITE Patterns/Profiles
1: BACTERIOFERRITIN (A:1-19,B:1-19,C:1-19,D:1-19,E:1-19...)
2: FERRITIN_LIKE (A:1-145,B:1-145,C:1-145,D:1-145,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BACTERIOFERRITIN
PS00549
Bacterioferritin signature.
BFR_AZOVI
1-19
24
A:1-19
B:1-19
C:1-19
D:1-19
E:1-19
F:1-19
G:1-19
H:1-19
2
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
BFR_AZOVI
1-145
24
A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145
G:1-145
H:1-145
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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, 8)
Info
All SCOP Domains
1a: SCOP_d2fl0a_ (A:)
1b: SCOP_d2fl0b_ (B:)
1c: SCOP_d2fl0c_ (C:)
1d: SCOP_d2fl0d_ (D:)
1e: SCOP_d2fl0e_ (E:)
1f: SCOP_d2fl0f_ (F:)
1g: SCOP_d2fl0g_ (G:)
1h: SCOP_d2fl0h_ (H:)
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Classes
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
automated matches
(70)
Azotobacter vinelandii [TaxId: 354]
(3)
1a
d2fl0a_
A:
1b
d2fl0b_
B:
1c
d2fl0c_
C:
1d
d2fl0d_
D:
1e
d2fl0e_
E:
1f
d2fl0f_
F:
1g
d2fl0g_
G:
1h
d2fl0h_
H:
[
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]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2fl0A00 (A:1-155)
1b: CATH_2fl0B00 (B:1-155)
1c: CATH_2fl0C00 (C:1-155)
1d: CATH_2fl0D00 (D:1-155)
1e: CATH_2fl0E00 (E:1-155)
1f: CATH_2fl0F00 (F:1-155)
1g: CATH_2fl0G00 (G:1-155)
1h: CATH_2fl0H00 (H:1-155)
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Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Azotobacter vinelandii. Organism_taxid: 354
(1)
1a
2fl0A00
A:1-155
1b
2fl0B00
B:1-155
1c
2fl0C00
C:1-155
1d
2fl0D00
D:1-155
1e
2fl0E00
E:1-155
1f
2fl0F00
F:1-155
1g
2fl0G00
G:1-155
1h
2fl0H00
H:1-155
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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