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3E1L
Biol. Unit 1
Info
Asym.Unit (339 KB)
Biol.Unit 1 (656 KB)
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Title
:
CRYSTAL STRUCTURE OF E. COLI BACTERIOFERRITIN (BFR) SOAKED IN PHOSPHATE WITH AN ALTERNATIVE CONFORMATION OF THE UNOCCUPIED FERROXIDASE CENTRE (APO-BFR II).
Authors
:
A. Crow, T. Lawson, A. Lewin, G. R. Moore, N. Le Brun
Date
:
04 Aug 08 (Deposition) - 05 May 09 (Release) - 26 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J,K,L (2x)
Keywords
:
Bacterioferritin. Rhombic Dodecahedral Superstructure, Heme, Iron, Iron Storage, Metal-Binding, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Crow, T. L. Lawson, A. Lewin, G. R. Moore, N. E. Le Brun
Structural Basis For Iron Mineralization By Bacterioferritin
J. Am. Chem. Soc. V. 131 6808 2009
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 44)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
12
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
SO4
32
Ligand/Ion
SULFATE ION
[
close Hetero Component info
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Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:145 , LEU A:146 , GLN A:147
BINDING SITE FOR RESIDUE SO4 A 250
02
AC2
SOFTWARE
ARG A:117 , ARG D:117 , ARG J:117
BINDING SITE FOR RESIDUE SO4 A 251
03
AC3
SOFTWARE
ILE A:22 , ASN A:23 , PHE A:26 , TYR A:45 , ILE A:49 , MET A:52 , ALA A:55 , ASP A:56 , LEU B:19 , ILE B:22 , ASN B:23 , PHE B:26 , TYR B:45 , ILE B:49 , MET B:52 , HOH B:265
BINDING SITE FOR RESIDUE HEM A 200
04
AC4
SOFTWARE
GLY B:145 , LEU B:146 , GLN B:147 , HOH B:253
BINDING SITE FOR RESIDUE SO4 B 250
05
AC5
SOFTWARE
ARG B:117 , ARG C:117 , ARG H:117
BINDING SITE FOR RESIDUE SO4 B 251
06
AC6
SOFTWARE
GLY C:145 , LEU C:146 , GLN C:147
BINDING SITE FOR RESIDUE SO4 C 250
07
AC7
SOFTWARE
ILE C:22 , ASN C:23 , PHE C:26 , TYR C:45 , ILE C:49 , MET C:52 , ALA C:55 , ASP C:56 , LEU D:19 , ILE D:22 , ASN D:23 , PHE D:26 , TYR D:45 , ILE D:49 , MET D:52 , HOH D:266
BINDING SITE FOR RESIDUE HEM C 200
08
AC8
SOFTWARE
GLY D:145 , LEU D:146 , GLN D:147
BINDING SITE FOR RESIDUE SO4 D 250
09
AC9
SOFTWARE
GLY E:145 , LEU E:146 , GLN E:147
BINDING SITE FOR RESIDUE SO4 E 250
10
BC1
SOFTWARE
ILE E:22 , ASN E:23 , PHE E:26 , TYR E:45 , ILE E:49 , MET E:52 , ALA E:55 , ASP E:56 , LEU F:19 , ILE F:22 , ASN F:23 , PHE F:26 , TYR F:45 , ILE F:49 , MET F:52 , HOH F:269
BINDING SITE FOR RESIDUE HEM E 200
11
BC2
SOFTWARE
GLY F:145 , LEU F:146 , GLN F:147
BINDING SITE FOR RESIDUE SO4 F 250
12
BC3
SOFTWARE
GLY G:145 , LEU G:146 , GLN G:147 , HOH G:271
BINDING SITE FOR RESIDUE SO4 G 250
13
BC4
SOFTWARE
ARG E:117 , ARG G:117 , ARG L:117
BINDING SITE FOR RESIDUE SO4 G 251
14
BC5
SOFTWARE
ILE G:22 , ASN G:23 , PHE G:26 , TYR G:45 , ILE G:49 , MET G:52 , ALA G:55 , ASP G:56 , LEU H:19 , ILE H:22 , ASN H:23 , PHE H:26 , TYR H:45 , ILE H:49 , MET H:52 , LYS H:53 , HOH H:273
BINDING SITE FOR RESIDUE HEM G 200
15
BC6
SOFTWARE
GLY H:145 , LEU H:146 , GLN H:147
BINDING SITE FOR RESIDUE SO4 H 250
16
BC7
SOFTWARE
GLY I:145 , LEU I:146 , GLN I:147
BINDING SITE FOR RESIDUE SO4 I 250
17
BC8
SOFTWARE
ILE I:22 , ASN I:23 , PHE I:26 , TYR I:45 , ILE I:49 , MET I:52 , ALA I:55 , ASP I:56 , LEU J:19 , ILE J:22 , ASN J:23 , PHE J:26 , TYR J:45 , ILE J:49 , MET J:52 , HOH J:273
BINDING SITE FOR RESIDUE HEM I 200
18
BC9
SOFTWARE
GLY J:145 , LEU J:146 , GLN J:147
BINDING SITE FOR RESIDUE SO4 J 250
19
CC1
SOFTWARE
GLY K:145 , LEU K:146 , GLN K:147
BINDING SITE FOR RESIDUE SO4 K 250
20
CC2
SOFTWARE
ARG F:117 , ARG I:117 , ARG K:117
BINDING SITE FOR RESIDUE SO4 K 251
21
CC3
SOFTWARE
ILE K:22 , ASN K:23 , PHE K:26 , TYR K:45 , ILE K:49 , MET K:52 , ALA K:55 , ASP K:56 , LEU L:19 , ILE L:22 , ASN L:23 , PHE L:26 , TYR L:45 , ILE L:49 , MET L:52 , HOH L:267
BINDING SITE FOR RESIDUE HEM K 200
22
CC4
SOFTWARE
GLY L:145 , LEU L:146 , GLN L:147
BINDING SITE FOR RESIDUE SO4 L 250
[
close Site info
]
SAPs(SNPs)/Variants
(10, 240)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_BFR_ECOLI_001 (K38M, chain A/B/C/D/E/F/G/H/I/J/K/L, )
02: VAR_BFR_ECOLI_002 (R57K, chain A/B/C/D/E/F/G/H/I/J/K/L, )
03: VAR_BFR_ECOLI_003 (L68I, chain A/B/C/D/E/F/G/H/I/J/K/L, )
04: VAR_BFR_ECOLI_004 (N78G, chain A/B/C/D/E/F/G/H/I/J/K/L, )
05: VAR_BFR_ECOLI_005 (R88Q, chain A/B/C/D/E/F/G/H/I/J/K/L, )
06: VAR_BFR_ECOLI_006 (A92R, chain A/B/C/D/E/F/G/H/I/J/K/L, )
07: VAR_BFR_ECOLI_007 (D96E, chain A/B/C/D/E/F/G/H/I/J/K/L, )
08: VAR_BFR_ECOLI_008 (N100D, chain A/B/C/D/E/F/G/H/I/J/K/L, )
09: VAR_BFR_ECOLI_009 (G106A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
10: VAR_BFR_ECOLI_010 (R125A, chain A/B/C/D/E/F/G/H/I/J/K/L, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_BFR_ECOLI_001
*
K
38
M
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
K
38
M
02
UniProt
VAR_BFR_ECOLI_002
*
R
57
K
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
57
K
03
UniProt
VAR_BFR_ECOLI_003
*
L
68
I
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
L
68
I
04
UniProt
VAR_BFR_ECOLI_004
*
N
78
G
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
78
G
05
UniProt
VAR_BFR_ECOLI_005
*
R
88
Q
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
88
Q
06
UniProt
VAR_BFR_ECOLI_006
*
A
92
R
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
A
92
R
07
UniProt
VAR_BFR_ECOLI_007
*
D
96
E
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
D
96
E
08
UniProt
VAR_BFR_ECOLI_008
*
N
100
D
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
N
100
D
09
UniProt
VAR_BFR_ECOLI_009
*
G
106
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
G
106
A
10
UniProt
VAR_BFR_ECOLI_010
*
R
125
A
BFR_ECOLI
---
---
A/B/C/D/E/F/G/H/I/J/K/L
R
125
A
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
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_ECOLI
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
I:1-19
J:1-19
K:1-19
L:1-19
2
FERRITIN_LIKE
PS50905
Ferritin-like diiron domain profile.
BFR_ECOLI
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
I:1-145
J:1-145
K:1-145
L:1-145
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3e1la_ (A:)
1b: SCOP_d3e1lb_ (B:)
1c: SCOP_d3e1lc_ (C:)
1d: SCOP_d3e1ld_ (D:)
1e: SCOP_d3e1le_ (E:)
1f: SCOP_d3e1lf_ (F:)
1g: SCOP_d3e1lg_ (G:)
1h: SCOP_d3e1lh_ (H:)
1i: SCOP_d3e1li_ (I:)
1j: SCOP_d3e1lj_ (J:)
1k: SCOP_d3e1lk_ (K:)
1l: SCOP_d3e1ll_ (L:)
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(
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Organisms
(
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(
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Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ferritin
(232)
Protein domain
:
Bacterioferritin (cytochrome b1)
(19)
Escherichia coli [TaxId: 562]
(11)
1a
d3e1la_
A:
1b
d3e1lb_
B:
1c
d3e1lc_
C:
1d
d3e1ld_
D:
1e
d3e1le_
E:
1f
d3e1lf_
F:
1g
d3e1lg_
G:
1h
d3e1lh_
H:
1i
d3e1li_
I:
1j
d3e1lj_
J:
1k
d3e1lk_
K:
1l
d3e1ll_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3e1lA00 (A:1-158)
1b: CATH_3e1lB00 (B:1-158)
1c: CATH_3e1lC00 (C:1-158)
1d: CATH_3e1lD00 (D:1-158)
1e: CATH_3e1lE00 (E:1-158)
1f: CATH_3e1lF00 (F:1-158)
1g: CATH_3e1lG00 (G:1-158)
1h: CATH_3e1lH00 (H:1-158)
1i: CATH_3e1lI00 (I:1-158)
1j: CATH_3e1lJ00 (J:1-158)
1k: CATH_3e1lK00 (K:1-158)
1l: CATH_3e1lL00 (L:1-158)
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)
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)
Escherichia coli. Organism_taxid: 83333. Strain: k-12.
(7)
1a
3e1lA00
A:1-158
1b
3e1lB00
B:1-158
1c
3e1lC00
C:1-158
1d
3e1lD00
D:1-158
1e
3e1lE00
E:1-158
1f
3e1lF00
F:1-158
1g
3e1lG00
G:1-158
1h
3e1lH00
H:1-158
1i
3e1lI00
I:1-158
1j
3e1lJ00
J:1-158
1k
3e1lK00
K:1-158
1l
3e1lL00
L:1-158
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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