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3MYR
Biol. Unit 4
Info
Asym.Unit (1.1 MB)
Biol.Unit 1 (277 KB)
Biol.Unit 2 (279 KB)
Biol.Unit 3 (279 KB)
Biol.Unit 4 (280 KB)
Biol.Unit 5 (546 KB)
Biol.Unit 6 (548 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF [NIFE] HYDROGENASE FROM ALLOCHROMATIUM VINOSUM IN ITS NI-A STATE
Authors
:
H. Ogata, P. Kellers, W. Lubitz
Date
:
11 May 10 (Deposition) - 04 Aug 10 (Release) - 06 Oct 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: E,F (1x)
Biol. Unit 4: G,H (1x)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: E,F,G,H (1x)
Keywords
:
[Nife] Hydrogenase, Allochromatium Vinosum, Photosynthetic Purple- Sulfur Bacterium, Iron-Sulfur Cluster, Ni-A State, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ogata, P. Kellers, W. Lubitz
The Crystal Structure Of The [Nife] Hydrogenase From The Photosynthetic Bacterium Allochromatium Vinosum: Characterization Of The Oxidized Enzyme (Ni-A State).
J. Mol. Biol. V. 402 428 2010
[
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Hetero Components
(4, 5)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: FE3-S4 CLUSTER (F3Sa)
2b: FE3-S4 CLUSTER (F3Sb)
2c: FE3-S4 CLUSTER (F3Sc)
2d: FE3-S4 CLUSTER (F3Sd)
3a: IMIDAZOLE (IMDa)
3b: IMIDAZOLE (IMDb)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
5a: NI-FE OXIDIZED ACTIVE CENTER (NFVa)
5b: NI-FE OXIDIZED ACTIVE CENTER (NFVb)
5c: NI-FE OXIDIZED ACTIVE CENTER (NFVc)
5d: NI-FE OXIDIZED ACTIVE CENTER (NFVd)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
6g: IRON/SULFUR CLUSTER (SF4g)
6h: IRON/SULFUR CLUSTER (SF4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
3
IMD
1
Ligand/Ion
IMIDAZOLE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NFV
1
Ligand/Ion
NI-FE OXIDIZED ACTIVE CENTER
6
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(8, 8)
Info
All Sites
1: AC4 (SOFTWARE)
2: CC2 (SOFTWARE)
3: CC3 (SOFTWARE)
4: CC4 (SOFTWARE)
5: CC5 (SOFTWARE)
6: CC6 (SOFTWARE)
7: CC7 (SOFTWARE)
8: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
VAL A:143 , ASN A:145 , GLY A:176 , HOH A:3657 , ARG G:139 , HOH G:5826
BINDING SITE FOR RESIDUE IMD A 3002
2
CC2
SOFTWARE
GLU G:15 , CYS G:16 , THR G:17 , GLY G:18 , CYS G:19 , ASP G:75 , GLY G:113 , THR G:114 , CYS G:115 , GLY G:148 , CYS G:149 , PRO G:150 , HIS H:1214
BINDING SITE FOR RESIDUE SF4 G 2001
3
CC3
SOFTWARE
HIS G:187 , CYS G:190 , ARG G:192 , ARG G:193 , CYS G:215 , LEU G:216 , CYS G:221
BINDING SITE FOR RESIDUE SF4 G 2002
4
CC4
SOFTWARE
ASN G:228 , CYS G:230 , TRP G:235 , TRP G:241 , CYS G:249 , LEU G:250 , CYS G:252 , LYS H:1211
BINDING SITE FOR RESIDUE F3S G 2003
5
CC5
SOFTWARE
PRO G:153 , MET G:154 , ASN G:236 , ASP G:237 , HOH G:3053
BINDING SITE FOR RESIDUE CL G 2004
6
CC6
SOFTWARE
ARG A:139 , HOH A:4142 , MET G:135 , VAL G:143 , ASN G:145 , GLY G:176 , HOH G:4119
BINDING SITE FOR RESIDUE IMD G 3001
7
CC7
SOFTWARE
CYS H:1061 , CYS H:1064 , VAL H:1067 , HIS H:1068 , ALA H:1485 , PRO H:1486 , ARG H:1487 , LEU H:1490 , VAL H:1508 , PRO H:1509 , SER H:1510 , CYS H:1555 , CYS H:1558
BINDING SITE FOR RESIDUE NFV H 2005
8
CC8
SOFTWARE
GLU H:1042 , ALA H:1506 , HIS H:1561 , HOH H:2007 , HOH H:2008 , HOH H:2009
BINDING SITE FOR RESIDUE MG H 2006
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
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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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d3myra_ (A:)
1b: SCOP_d3myrc_ (C:)
1c: SCOP_d3myre_ (E:)
1d: SCOP_d3myrg_ (G:)
2a: SCOP_d3myrb_ (B:)
2b: SCOP_d3myrd_ (D:)
2c: SCOP_d3myrf_ (F:)
2d: SCOP_d3myrh_ (H:)
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)
(
)
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(
)
(
)
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)
(
)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
automated matches
(8)
Protein domain
:
automated matches
(8)
Allochromatium vinosum [TaxId: 1049]
(1)
1a
d3myra_
A:
1b
d3myrc_
C:
1c
d3myre_
E:
1d
d3myrg_
G:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Allochromatium vinosum [TaxId: 1049]
(1)
2a
d3myrb_
B:
2b
d3myrd_
D:
2c
d3myrf_
F:
2d
d3myrh_
H:
[
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CATH Domains
(0, 0)
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all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_NiFeSe_Hases_3myrH01 (H:1039-1561)
1b: PFAM_NiFeSe_Hases_3myrH02 (H:1039-1561)
1c: PFAM_NiFeSe_Hases_3myrH03 (H:1039-1561)
1d: PFAM_NiFeSe_Hases_3myrH04 (H:1039-1561)
2a: PFAM_Oxidored_q6_3myrG01 (G:16-163)
2b: PFAM_Oxidored_q6_3myrG02 (G:16-163)
2c: PFAM_Oxidored_q6_3myrG03 (G:16-163)
2d: PFAM_Oxidored_q6_3myrG04 (G:16-163)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: NiFeSe_Hases]
(17)
Family
:
NiFeSe_Hases
(17)
Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / D) (Chromatium vinosum)
(1)
1a
NiFeSe_Hases-3myrH01
H:1039-1561
1b
NiFeSe_Hases-3myrH02
H:1039-1561
1c
NiFeSe_Hases-3myrH03
H:1039-1561
1d
NiFeSe_Hases-3myrH04
H:1039-1561
Clan
:
no clan defined [family: Oxidored_q6]
(18)
Family
:
Oxidored_q6
(18)
Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / D) (Chromatium vinosum)
(1)
2a
Oxidored_q6-3myrG01
G:16-163
2b
Oxidored_q6-3myrG02
G:16-163
2c
Oxidored_q6-3myrG03
G:16-163
2d
Oxidored_q6-3myrG04
G:16-163
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Asymmetric Unit 1
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Asym.Unit (1.1 MB)
Header - Asym.Unit
Biol.Unit 1 (277 KB)
Header - Biol.Unit 1
Biol.Unit 2 (279 KB)
Header - Biol.Unit 2
Biol.Unit 3 (279 KB)
Header - Biol.Unit 3
Biol.Unit 4 (280 KB)
Header - Biol.Unit 4
Biol.Unit 5 (546 KB)
Header - Biol.Unit 5
Biol.Unit 6 (548 KB)
Header - Biol.Unit 6
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