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3USC
Biol. Unit 3
Info
Asym.Unit (311 KB)
Biol.Unit 1 (153 KB)
Biol.Unit 2 (153 KB)
Biol.Unit 3 (300 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E. COLI HYDROGENASE-1 IN A FERRICYANIDE-OXIDIZED FORM
Authors
:
A. Volbeda, J. C. Fontecilla-Camps, C. Darnault
Date
:
23 Nov 11 (Deposition) - 28 Mar 12 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : L,M,S,T
Biol. Unit 1: L,S (1x)
Biol. Unit 2: M,T (1x)
Biol. Unit 3: L,M,S,T (1x)
Keywords
:
Membrane-Bound Hydrogenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Volbeda, P. Amara, C. Darnault, J. M. Mouesca, A. Parkin, M. M. Roessler, F. A. Armstrong, J. C. Fontecilla-Camps
X-Ray Crystallographic And Computational Studies Of The O2-Tolerant [Nife]-Hydrogenase 1 From Escherichia Coli.
Proc. Natl. Acad. Sci. Usa V. 109 5305 2012
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Hetero Components
(7, 16)
Info
All Hetero Components
1a: NICKEL (III) ION (3NIa)
1b: NICKEL (III) ION (3NIb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: FE3-S4 CLUSTER (F3Sa)
3b: FE3-S4 CLUSTER (F3Sb)
4a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
4b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
5a: LITHIUM ION (LIa)
6a: DODECYL-BETA-D-MALTOSIDE (LMTa)
6b: DODECYL-BETA-D-MALTOSIDE (LMTb)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
8a: FE4-S3 CLUSTER (SF3a)
8b: FE4-S3 CLUSTER (SF3b)
9a: IRON/SULFUR CLUSTER (SF4a)
9b: IRON/SULFUR CLUSTER (SF4b)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
10d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3NI
2
Ligand/Ion
NICKEL (III) ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
4
FCO
2
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
5
LI
-1
Ligand/Ion
LITHIUM ION
6
LMT
2
Ligand/Ion
DODECYL-BETA-D-MALTOSIDE
7
MG
-1
Ligand/Ion
MAGNESIUM ION
8
SF3
2
Ligand/Ion
FE4-S3 CLUSTER
9
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
10
SO4
4
Ligand/Ion
SULFATE ION
[
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , TYR S:217 , CYS S:221
BINDING SITE FOR RESIDUE SF4 S 401
02
AC2
SOFTWARE
LYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , CYS S:249 , LEU S:250 , CYS S:252
BINDING SITE FOR RESIDUE F3S S 402
03
AC3
SOFTWARE
GLU S:16 , CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , GLU S:76 , THR S:114 , CYS S:115 , CYS S:120 , GLY S:148 , CYS S:149
BINDING SITE FOR RESIDUE SF3 S 403
04
AC4
SOFTWARE
ILE S:7 , VAL S:9 , TRP S:11 , ILE S:160 , MET S:163
BINDING SITE FOR RESIDUE LMT S 404
05
AC5
SOFTWARE
THR S:114 , TRP S:118 , CYS S:120 , GLY S:256 , HOH S:547
BINDING SITE FOR RESIDUE CL S 405
06
AC6
SOFTWARE
ILE S:12 , HIS S:13 , ASP S:46 , LYS S:98 , HOH S:567 , HOH S:607
BINDING SITE FOR RESIDUE CL S 406
07
AC7
SOFTWARE
LEU L:482 , ALA L:483 , ARG S:211
BINDING SITE FOR RESIDUE SO4 S 407
08
AC8
SOFTWARE
CYS L:79 , VAL L:82 , HIS L:83 , ALA L:507 , PRO L:508 , ARG L:509 , LEU L:512 , VAL L:530 , PRO L:531 , THR L:532 , CYS L:579 , 3NI L:602 , HOH L:701
BINDING SITE FOR RESIDUE FCO L 601
09
AC9
SOFTWARE
CYS L:76 , CYS L:79 , CYS L:576 , CYS L:579 , FCO L:601 , HOH L:701
BINDING SITE FOR RESIDUE 3NI L 602
10
BC1
SOFTWARE
GLU L:57 , CYS L:528 , HIS L:582 , HOH L:703 , HOH L:704 , HOH L:705
BINDING SITE FOR RESIDUE MG L 603
11
BC2
SOFTWARE
ASN L:390 , GLN L:392 , HOH L:930
BINDING SITE FOR RESIDUE LI L 604
12
BC3
SOFTWARE
HIS T:187 , CYS T:190 , ARG T:193 , CYS T:215 , LEU T:216 , TYR T:217 , CYS T:221
BINDING SITE FOR RESIDUE SF4 T 401
13
BC4
SOFTWARE
LYS M:226 , THR T:226 , ASN T:228 , CYS T:230 , TRP T:235 , CYS T:249 , LEU T:250 , CYS T:252
BINDING SITE FOR RESIDUE F3S T 402
14
BC5
SOFTWARE
CYS T:17 , THR T:18 , CYS T:19 , CYS T:20 , GLU T:76 , THR T:114 , CYS T:115 , CYS T:120 , GLY T:148 , CYS T:149
BINDING SITE FOR RESIDUE SF3 T 403
15
BC6
SOFTWARE
ILE T:7 , TRP T:11 , MET T:163 , ASP T:167 , ARG T:168
BINDING SITE FOR RESIDUE LMT T 404
16
BC7
SOFTWARE
TRP T:118 , CYS T:120 , GLY T:256
BINDING SITE FOR RESIDUE CL T 405
17
BC8
SOFTWARE
ILE T:12 , HIS T:13 , ASP T:46 , LYS T:98 , HOH T:580 , HOH T:620
BINDING SITE FOR RESIDUE CL T 406
18
BC9
SOFTWARE
ASP T:173 , ARG T:174
BINDING SITE FOR RESIDUE CL T 407
19
CC1
SOFTWARE
LYS L:171 , LEU M:482 , ALA M:483 , ARG T:211
BINDING SITE FOR RESIDUE SO4 T 408
20
CC2
SOFTWARE
LYS T:218 , ARG T:266
BINDING SITE FOR RESIDUE SO4 T 409
21
CC3
SOFTWARE
CYS M:79 , VAL M:82 , HIS M:83 , ALA M:507 , PRO M:508 , ARG M:509 , LEU M:512 , VAL M:530 , PRO M:531 , THR M:532 , CYS M:579 , 3NI M:602 , HOH M:702
BINDING SITE FOR RESIDUE FCO M 601
22
CC4
SOFTWARE
CYS M:76 , CYS M:79 , CYS M:576 , CYS M:579 , FCO M:601 , HOH M:702
BINDING SITE FOR RESIDUE 3NI M 602
23
CC5
SOFTWARE
GLU M:57 , CYS M:528 , HIS M:582 , HOH M:704 , HOH M:705 , HOH M:706
BINDING SITE FOR RESIDUE MG M 603
24
CC6
SOFTWARE
ARG M:394 , ARG S:125
BINDING SITE FOR RESIDUE SO4 M 604
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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, 4)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (L:54-79,M:54-79)
2: NI_HGENASE_L_2 (L:573-582,M:573-582)
;
View:
Select:
Label:
End label:
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_ECOLI
54-79
2
L:54-79
M:54-79
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
MBHL_ECOLI
573-582
2
L:573-582
M:573-582
[
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3uscs_ (S:)
1b: SCOP_d3usct_ (T:)
2a: SCOP_d3uscl_ (L:)
2b: SCOP_d3uscm_ (M:)
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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)
Escherichia coli [TaxId: 562]
(3)
1a
d3uscs_
S:
1b
d3usct_
T:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Escherichia coli [TaxId: 562]
(3)
2a
d3uscl_
L:
2b
d3uscm_
M:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Atom Selection
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Sidechain
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain S
Chain T
Asymmetric Unit 1
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