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3RGW
Asym. Unit
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Asym.Unit (303 KB)
Biol.Unit 1 (296 KB)
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(1)
Title
:
CRYSTAL STRUCTURE AT 1.5 A RESOLUTION OF AN H2-REDUCED, O2-TOLERANT HYDROGENASE FROM RALSTONIA EUTROPHA UNMASKS A NOVEL IRON-SULFUR CLUSTER
Authors
:
P. Scheerer, J. Fritsch, S. Frielingsdorf, S. Kroschinsky, B. Friedri O. Lenz, C. M. T. Spahn
Date
:
10 Apr 11 (Deposition) - 26 Oct 11 (Release) - 23 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : L,S
Biol. Unit 1: L,S (1x)
Keywords
:
[Nife] Hydrogenase, High-Resolution Crystal Structure, Knallgasbacteria, Proteobacteria, Aerobic Hydrogen Bacteria, Dehydrogenase, Oxidoreductase, Hydrogen, Dihydrogen, Hydrogen Catalysis, Metalloenzyme, Metalloprotein Catalytic Center, Nickel, Iron, Nickel-Iron Cofactor, Bimetallic, Ni-Fe Active Site, Iron- Sulfur Cluster, T-Cluster, [4Fe-3S] Cluster, [3Fe-4S] Cluster, [4Fe- 4S] Cluster, Reduced State, Oxygen-Tolerant Hydrogenase, Membrane, Membrane-Bound, Oxidoreductase-Oxidoreductase Complex
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Reference
:
J. Fritsch, P. Scheerer, S. Frielingsdorf, S. Kroschinsky, B. Friedrich, O. Lenz, C. M. Spahn
The Crystal Structure Of An Oxygen-Tolerant Hydrogenase Uncovers A Novel Iron-Sulphur Centre.
Nature V. 479 249 2011
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Hetero Components
(5, 5)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
2a: FE4-S3 CLUSTER (F4Sa)
3a: MAGNESIUM ION (MGa)
4a: FORMYL[BIS(HYDROCYANATO-1KAPPAC)]I... (NFUa)
5a: IRON/SULFUR CLUSTER (SF4a)
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No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
F4S
1
Ligand/Ion
FE4-S3 CLUSTER
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
NFU
1
Ligand/Ion
FORMYL[BIS(HYDROCYANATO-1KAPPAC)]IRONNICKEL(FE-NI)
5
SF4
1
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS L:75 , CYS L:78 , CYS L:81 , HIS L:82 , ALA L:528 , PRO L:529 , ARG L:530 , LEU L:533 , VAL L:551 , PRO L:552 , THR L:553 , CYS L:597 , CYS L:600
BINDING SITE FOR RESIDUE NFU L 1004
2
AC2
SOFTWARE
GLU L:56 , CYS L:549 , HIS L:603 , HOH L:668 , HOH L:726 , HOH L:877
BINDING SITE FOR RESIDUE MG L 1005
3
AC3
SOFTWARE
HIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221 , ILE S:243
BINDING SITE FOR RESIDUE SF4 S 1001
4
AC4
SOFTWARE
LYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , PRO S:242 , CYS S:249 , ILE S:250 , CYS S:252
BINDING SITE FOR RESIDUE F3S S 1002
5
AC5
SOFTWARE
CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , SER S:114 , CYS S:115 , CYS S:120 , CYS S:149
BINDING SITE FOR RESIDUE F4S S 1003
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SAPs(SNPs)/Variants
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (L:53-78)
2: NI_HGENASE_L_2 (L:594-603)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NI_HGENASE_L_1
PS00507
Nickel-dependent hydrogenases large subunit signature 1.
MBHL_CUPNH
53-78
1
L:53-78
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
MBHL_CUPNH
594-603
1
L:594-603
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Exons
(0, 0)
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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
(2, 2)
Info
All SCOP Domains
1a: SCOP_d3rgws_ (S:)
2a: SCOP_d3rgwl_ (L:)
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Protein Domains
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Organisms
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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)
Ralstonia eutropha [TaxId: 381666]
(1)
1a
d3rgws_
S:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Ralstonia eutropha [TaxId: 381666]
(4)
2a
d3rgwl_
L:
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CATH Domains
(0, 0)
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (303 KB)
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