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Asym. Unit
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Asym.Unit (221 KB)
Biol.Unit 1 (627 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE AZOTOBACTER VINELANDII BACTERIOFERRITIN AT 2.6 A RESOLUTION
Authors
:
H. L. Liu, J. F. Huang, R. C. Bi
Date
:
14 Mar 04 (Deposition) - 05 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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, Active As 24-Mer, Four-Helix Bundle, Electron Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Liu, H. N. Zhou, W. M. Xing, J. F. Zhao, S. X. Li, J. F. Huang, R. C. Bi
2. 6 A Resolution Crystal Structure Of The Bacterioferritin From Azotobacter Vinelandii
Febs Lett. V. 573 93 2004
[
close entry info
]
Hetero Components
(4, 32)
Info
All Hetero Components
1a: BARIUM ION (BAa)
1b: BARIUM ION (BAb)
2a: FE (II) ION (FE2a)
2b: FE (II) ION (FE2b)
2c: FE (II) ION (FE2c)
2d: FE (II) ION (FE2d)
2e: FE (II) ION (FE2e)
2f: FE (II) ION (FE2f)
2g: FE (II) ION (FE2g)
2h: FE (II) ION (FE2h)
2i: FE (II) ION (FE2i)
2j: FE (II) ION (FE2j)
2k: FE (II) ION (FE2k)
2l: FE (II) ION (FE2l)
2m: FE (II) ION (FE2m)
2n: FE (II) ION (FE2n)
2o: FE (II) ION (FE2o)
2p: FE (II) ION (FE2p)
3a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
3b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
3c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
3d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BA
2
Ligand/Ion
BARIUM ION
2
FE2
16
Ligand/Ion
FE (II) ION
3
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
4
MG
10
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:18 , GLU A:51 , HIS A:54 , GLU A:127
BINDING SITE FOR RESIDUE FE2 A 202
02
AC2
SOFTWARE
GLU B:18 , GLU B:51 , HIS B:54 , GLU B:127
BINDING SITE FOR RESIDUE FE2 B 202
03
AC3
SOFTWARE
GLU C:18 , GLU C:51 , HIS C:54 , ILE C:123 , GLU C:127
BINDING SITE FOR RESIDUE FE2 C 202
04
AC4
SOFTWARE
GLU D:18 , GLU D:51 , HIS D:54 , GLU D:127
BINDING SITE FOR RESIDUE FE2 D 202
05
AC5
SOFTWARE
GLU E:18 , GLU E:51 , HIS E:54 , GLU E:127
BINDING SITE FOR RESIDUE FE2 E 202
06
AC6
SOFTWARE
GLU F:18 , GLU F:51 , HIS F:54 , GLU F:127
BINDING SITE FOR RESIDUE FE2 F 202
07
AC7
SOFTWARE
GLU G:18 , GLU G:51 , HIS G:54 , GLU G:127
BINDING SITE FOR RESIDUE FE2 G 202
08
AC8
SOFTWARE
GLU H:18 , GLU H:51 , HIS H:54 , GLU H:127
BINDING SITE FOR RESIDUE FE2 H 202
09
AC9
SOFTWARE
GLU A:51 , GLU A:94 , GLU A:127 , HIS A:130 , HOH A:421
BINDING SITE FOR RESIDUE FE2 A 201
10
BC1
SOFTWARE
GLU B:51 , GLU B:94 , GLU B:127 , HOH B:1203 , HOH B:1204
BINDING SITE FOR RESIDUE FE2 B 201
11
BC2
SOFTWARE
GLU C:51 , GLU C:94 , GLU C:127 , HIS C:130
BINDING SITE FOR RESIDUE FE2 C 201
12
BC3
SOFTWARE
GLU D:51 , GLU D:94 , GLU D:127 , HIS D:130 , HOH D:512 , HOH D:514
BINDING SITE FOR RESIDUE FE2 D 201
13
BC4
SOFTWARE
GLU E:51 , GLU E:94 , GLU E:127 , HIS E:130 , HOH E:3208
BINDING SITE FOR RESIDUE FE2 E 201
14
BC5
SOFTWARE
GLU F:51 , GLU F:94 , GLU F:127 , HOH F:318
BINDING SITE FOR RESIDUE FE2 F 201
15
BC6
SOFTWARE
GLU G:51 , GLU G:94 , GLU G:127 , HOH G:4213 , HOH G:4229
BINDING SITE FOR RESIDUE FE2 G 201
16
BC7
SOFTWARE
GLU H:51 , GLU H:94 , GLU H:127 , HIS H:130 , HOH H:312 , HOH H:330
BINDING SITE FOR RESIDUE FE2 H 201
17
BC8
SOFTWARE
GLU D:81 , GLU D:85 , HOH D:524 , GLU H:85
BINDING SITE FOR RESIDUE MG D 501
18
BC9
SOFTWARE
GLU C:85 , GLU G:81 , GLU G:85 , HOH G:4233
BINDING SITE FOR RESIDUE MG G 502
19
CC1
SOFTWARE
ASP A:132 , GLU A:135 , HOH A:409 , HOH A:411 , HOH A:419 , HOH A:423
BINDING SITE FOR RESIDUE MG A 301
20
CC2
SOFTWARE
HOH B:1217 , HOH B:1218 , HOH B:1220 , ASP D:34
BINDING SITE FOR RESIDUE MG D 302
21
CC3
SOFTWARE
HOH C:2203 , HOH C:2229 , ASP E:34
BINDING SITE FOR RESIDUE MG C 303
22
CC4
SOFTWARE
HOH D:507 , HOH D:516 , HOH D:523 , HOH D:528
BINDING SITE FOR RESIDUE MG D 304
23
CC5
SOFTWARE
ASP B:34 , HOH B:1201 , HOH E:3220
BINDING SITE FOR RESIDUE MG B 305
24
CC6
SOFTWARE
HOH A:424 , HOH B:1216 , HOH F:316
BINDING SITE FOR RESIDUE MG F 306
25
CC7
SOFTWARE
ASP F:34 , HOH F:308 , ASP G:132 , HOH G:4204 , HOH G:4214
BINDING SITE FOR RESIDUE MG F 307
26
CC8
SOFTWARE
HOH G:4206 , HOH G:4210 , HOH G:4216 , HOH G:4226 , HOH G:4232 , HOH H:322
BINDING SITE FOR RESIDUE MG H 308
27
CC9
SOFTWARE
ASN B:148 , GLN B:151 , ASN C:148 , GLN C:151 , ASN D:148 , GLN D:151 , ASN E:148 , GLN E:151
BINDING SITE FOR RESIDUE BA D 401
28
DC1
SOFTWARE
ASN A:148 , GLN A:151 , ASN F:148 , GLN F:151 , ASN G:148 , GLN G:151 , ASN H:148 , GLN H:151
BINDING SITE FOR RESIDUE BA A 402
29
DC2
SOFTWARE
ASN A:23 , PHE A:26 , TYR A:45 , ILE A:49 , MET A:52 , LYS A:53 , ALA A:55 , ASP A:56 , LEU B:19 , ILE B:22 , ASN B:23 , PHE B:26 , TYR B:45 , MET B:52
BINDING SITE FOR RESIDUE HEM B 1200
30
DC3
SOFTWARE
ASN C:23 , PHE C:26 , TYR C:45 , MET C:52 , LYS C:53 , ASP C:56 , ASN D:23 , PHE D:26 , TYR D:45 , MET D:52 , LYS D:53
BINDING SITE FOR RESIDUE HEM C 2200
31
DC4
SOFTWARE
ASN E:23 , PHE E:26 , TYR E:45 , MET E:52 , LYS E:53 , ILE E:59 , PHE F:26 , TYR F:45 , MET F:52 , LYS F:53
BINDING SITE FOR RESIDUE HEM E 3200
32
DC5
SOFTWARE
ASN G:23 , PHE G:26 , TYR G:45 , MET G:52 , ALA G:55 , PHE H:26 , TYR H:45 , MET H:52 , LYS H:53
BINDING SITE FOR RESIDUE HEM G 4200
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 16)
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
8
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
8
A:1-145
B:1-145
C:1-145
D:1-145
E:1-145
F:1-145
G:1-145
H:1-145
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
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Label:
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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1sofb_ (B:)
1b: SCOP_d1sofd_ (D:)
1c: SCOP_d1sofe_ (E:)
1d: SCOP_d1soff_ (F:)
1e: SCOP_d1sofg_ (G:)
1f: SCOP_d1sofh_ (H:)
1g: SCOP_d1sofc_ (C:)
2a: SCOP_d1sofa1 (A:1-154)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1sofb_
B:
1b
d1sofd_
D:
1c
d1sofe_
E:
1d
d1soff_
F:
1e
d1sofg_
G:
1f
d1sofh_
H:
1g
d1sofc_
C:
Protein domain
:
Bacterioferritin (cytochrome b1)
(19)
Azotobacter vinelandii [TaxId: 354]
(1)
2a
d1sofa1
A:1-154
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1sofA00 (A:1-155)
1b: CATH_1sofC00 (C:1-155)
1c: CATH_1sofD00 (D:1-155)
1d: CATH_1sofE00 (E:1-155)
1e: CATH_1sofF00 (F:1-155)
1f: CATH_1sofG00 (G:1-155)
1g: CATH_1sofH00 (H:1-155)
1h: CATH_1sofB00 (B:1-155)
View:
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)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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. Strain: uw3
(2)
1a
1sofA00
A:1-155
1b
1sofC00
C:1-155
1c
1sofD00
D:1-155
1d
1sofE00
E:1-155
1e
1sofF00
F:1-155
1f
1sofG00
G:1-155
1g
1sofH00
H:1-155
1h
1sofB00
B:1-155
[
close CATH info
]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Ferritin_1sofH01 (H:8-144)
1b: PFAM_Ferritin_1sofH02 (H:8-144)
1c: PFAM_Ferritin_1sofH03 (H:8-144)
1d: PFAM_Ferritin_1sofH04 (H:8-144)
1e: PFAM_Ferritin_1sofH05 (H:8-144)
1f: PFAM_Ferritin_1sofH06 (H:8-144)
1g: PFAM_Ferritin_1sofH07 (H:8-144)
1h: PFAM_Ferritin_1sofH08 (H:8-144)
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Clans
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(
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Families
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(
)
Organisms
(
)
(
)
Clan
:
Ferritin
(185)
Family
:
Ferritin
(83)
Azotobacter vinelandii
(1)
1a
Ferritin-1sofH01
H:8-144
1b
Ferritin-1sofH02
H:8-144
1c
Ferritin-1sofH03
H:8-144
1d
Ferritin-1sofH04
H:8-144
1e
Ferritin-1sofH05
H:8-144
1f
Ferritin-1sofH06
H:8-144
1g
Ferritin-1sofH07
H:8-144
1h
Ferritin-1sofH08
H:8-144
[
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]
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