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3CUR
Biol. Unit 3
Info
Asym.Unit (405 KB)
Biol.Unit 1 (137 KB)
Biol.Unit 2 (136 KB)
Biol.Unit 3 (136 KB)
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(1)
Title
:
STRUCTURE OF A DOUBLE METHIONINE MUTANT OF NI-FE HYDROGENASE
Authors
:
A. Volbeda
Date
:
17 Apr 08 (Deposition) - 05 Aug 08 (Release) - 07 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,H,I,J
Biol. Unit 1: A,H (1x)
Biol. Unit 2: B,I (1x)
Biol. Unit 3: C,J (1x)
Keywords
:
Ni-Fe Hydrogenase Tunnel Mutant, Iron, Iron-Sulfur, Metal-Binding, Oxidoreductase, Nickel
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Leroux, S. Dementin, B. Burlat, L. Cournac, A. Volbeda, S. Champ, L. Martin, B. Guigliarelli, P. Bertrand, J. Fontecilla-Camps, M. Rousset
Experimental Approaches To Kinetics Of Gas Diffusion In Hydrogenase
Proc. Natl. Acad. Sci. Usa V. 105 11188 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 7)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
1c: FE3-S4 CLUSTER (F3Sc)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
2b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
2c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
5c: NICKEL (II) ION (NIc)
6a: PEROXIDE ION (PERa)
6b: PEROXIDE ION (PERb)
6c: PEROXIDE ION (PERc)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
7e: IRON/SULFUR CLUSTER (SF4e)
7f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
FCO
1
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
3
GOL
2
Ligand/Ion
GLYCEROL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
NI
-1
Ligand/Ion
NICKEL (II) ION
6
PER
1
Ligand/Ion
PEROXIDE ION
7
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
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]
Sites
(10, 10)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC6 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC5 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
CYS J:72 , CYS J:75 , CYS J:543 , CYS J:546
BINDING SITE FOR RESIDUE NI J 551
02
AC6
SOFTWARE
GLU J:53 , LEU J:495 , HIS J:549 , HOH J:567 , HOH J:568 , HOH J:569
BINDING SITE FOR RESIDUE MG J 553
03
BC8
SOFTWARE
HIS C:184 , CYS C:187 , ARG C:189 , LEU C:190 , CYS C:212 , LEU C:213 , CYS C:218 , PRO C:221
BINDING SITE FOR RESIDUE SF4 C 265
04
BC9
SOFTWARE
THR C:223 , ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , GLN J:230
BINDING SITE FOR RESIDUE F3S C 266
05
CC1
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , PRO C:148 , ARG J:70 , HIS J:228
BINDING SITE FOR RESIDUE SF4 C 267
06
CC2
SOFTWARE
CYS J:75 , HIS J:79 , ALA J:474 , PRO J:475 , ARG J:476 , LEU J:479 , PRO J:498 , SER J:499 , CYS J:546
BINDING SITE FOR RESIDUE FCO J 550
07
CC3
SOFTWARE
CYS J:75 , ARG J:476 , CYS J:543 , CYS J:546
BINDING SITE FOR RESIDUE PER J 552
08
CC5
SOFTWARE
ALA A:55 , HOH C:270 , ASN H:181 , ALA H:182 , TYR H:183 , LEU H:185 , ARG H:529 , HOH H:640
BINDING SITE FOR RESIDUE GOL H 562
09
CC9
SOFTWARE
GLY J:450 , LYS J:452 , ASP J:453 , ASN J:454 , HOH J:714
BINDING SITE FOR RESIDUE GOL J 564
10
DC1
SOFTWARE
ARG J:100 , ASN J:104 , PHE J:295 , ALA J:296 , THR J:297 , TRP J:442 , GLU J:445 , HOH J:582 , HOH J:630 , HOH J:653
BINDING SITE FOR RESIDUE GOL J 565
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (J:50-75)
2: NI_HGENASE_L_2 (J:540-549)
;
View:
Select:
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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.
PHNL_DESFR
50-75
1
-
-
J:50-75
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
1
-
-
J:540-549
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3cura_ (A:)
1b: SCOP_d3curb_ (B:)
1c: SCOP_d3curc_ (C:)
2a: SCOP_d3curh_ (H:)
2b: SCOP_d3curi_ (I:)
2c: SCOP_d3curj_ (J:)
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(
)
(
)
Folds
(
)
(
)
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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
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
1a
d3cura_
A:
1b
d3curb_
B:
1c
d3curc_
C:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
2a
d3curh_
H:
2b
d3curi_
I:
2c
d3curj_
J:
[
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CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_3curA01 (A:3-178)
1b: CATH_3curB01 (B:3-178)
1c: CATH_3curC01 (C:5-178)
2a: CATH_3curA02 (A:179-263)
2b: CATH_3curB02 (B:179-263)
2c: CATH_3curC02 (C:179-263)
3a: CATH_3curH00 (H:5-549)
3b: CATH_3curI00 (I:5-549)
3c: CATH_3curJ00 (J:5-549)
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(
)
(
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.700, no name defined]
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
1a
3curA01
A:3-178
1b
3curB01
B:3-178
1c
3curC01
C:5-178
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome-c3 Hydrogenase; Chain A, domain 2
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain A, domain 2
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
2a
3curA02
A:179-263
2b
3curB02
B:179-263
2c
3curC02
C:179-263
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
3a
3curH00
H:5-549
3b
3curI00
I:5-549
3c
3curJ00
J:5-549
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain C
Chain J
Asymmetric Unit 1
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