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1FRV
Asym. Unit
Info
Asym.Unit (258 KB)
Biol.Unit 1 (127 KB)
Biol.Unit 2 (126 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
Authors
:
A. Volbeda, M. Frey, J. C. Fontecilla-Camps
Date
:
28 Mar 96 (Deposition) - 08 Nov 96 (Release) - 24 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Ni-Fe Hydrogenase, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
Reference
:
A. Volbeda, M. H. Charon, C. Piras, E. C. Hatchikian, M. Frey, J. C. Fontecilla-Camps
Crystal Structure Of The Nickel-Iron Hydrogenase From Desulfovibrio Gigas.
Nature V. 373 580 1995
(for further references see the
PDB file header
)
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Hetero Components
(4, 10)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
2a: HYDRATED FE (FELa)
2b: HYDRATED FE (FELb)
3a: NICKEL (II) ION (NIa)
3b: NICKEL (II) ION (NIb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
4c: IRON/SULFUR CLUSTER (SF4c)
4d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
2
Ligand/Ion
FE3-S4 CLUSTER
2
FEL
2
Ligand/Ion
HYDRATED FE
3
NI
2
Ligand/Ion
NICKEL (II) ION
4
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
[
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Sites
(12, 12)
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: CT1 (UNKNOWN)
12: CT2 (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS B:65 , VAL B:67 , CYS B:68 , CYS B:530 , CYS B:533 , FEL B:537
BINDING SITE FOR RESIDUE NI B 538
02
AC2
SOFTWARE
CYS D:65 , CYS D:68 , CYS D:530 , CYS D:533 , FEL D:537
BINDING SITE FOR RESIDUE NI D 538
03
AC3
SOFTWARE
VAL A:184 , HIS A:185 , CYS A:188 , ARG A:190 , CYS A:213 , LEU A:214 , CYS A:219 , GLY A:221 , VAL A:240
BINDING SITE FOR RESIDUE SF4 A 265
04
AC4
SOFTWARE
THR A:224 , ASN A:226 , CYS A:228 , PHE A:233 , TRP A:238 , PRO A:239 , CYS A:246 , ILE A:247 , CYS A:249 , LYS B:216 , GLN B:221
BINDING SITE FOR RESIDUE F3S A 266
05
AC5
SOFTWARE
CYS A:17 , GLY A:19 , CYS A:20 , GLY A:110 , THR A:111 , CYS A:112 , CYS A:148 , PRO A:149 , HIS B:219
BINDING SITE FOR RESIDUE SF4 A 267
06
AC6
SOFTWARE
CYS B:68 , HIS B:72 , ARG B:463 , VAL B:484 , SER B:486 , CYS B:533 , NI B:538
BINDING SITE FOR RESIDUE FEL B 537
07
AC7
SOFTWARE
HIS C:185 , CYS C:188 , ARG C:190 , LEU C:191 , CYS C:213 , LEU C:214 , CYS C:219
BINDING SITE FOR RESIDUE SF4 C 265
08
AC8
SOFTWARE
VAL C:184 , THR C:224 , ASN C:226 , CYS C:228 , PHE C:233 , TRP C:238 , CYS C:246 , ILE C:247 , CYS C:249 , GLN D:221
BINDING SITE FOR RESIDUE F3S C 266
09
AC9
SOFTWARE
CYS C:17 , CYS C:20 , THR C:111 , CYS C:112 , CYS C:148 , PRO C:149 , ARG D:63 , HIS D:219
BINDING SITE FOR RESIDUE SF4 C 267
10
BC1
SOFTWARE
CYS D:68 , VAL D:71 , HIS D:72 , ALA D:461 , VAL D:484 , SER D:486 , CYS D:533 , NI D:538
BINDING SITE FOR RESIDUE FEL D 537
11
CT1
UNKNOWN
CYS B:65 , CYS B:68 , CYS B:530 , CYS B:533 , FEL B:537 , NI B:538
THE ACTIVE SITE CONTAINS TWO METALS: NI AND (PROBABLY) FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY AN ANOMALOUS DIFFERENCE MAP AND BY A METAL ANALYSIS. THE PUTATIVE FE HAS 3 NON-PROTEIN LIGANDS (L) OF YET UNKNOWN IDENTITY. THESE LIGANDS WERE MODELED AS WATER DURING REFINEMENT. THE USED CRYSTALS MOST LIKELY CONTAIN A MIXTURE OF SEVERAL ACTIVE SITE REDOX STATES (SEE NATURE PUBLICATION). THE ACTUAL OXIDATION STATE OF THE NI AND PUTATIVE FE IN EACH OF THESE STATES IS STILL A MATTER OF INVESTIGATION. THE RESIDUES OF THE ACTIVE SITE ARE LISTED IN THE *SITE* RECORDS BELOW.
12
CT2
UNKNOWN
CYS D:65 , CYS D:68 , CYS D:530 , CYS D:533 , FEL D:537 , NI D:538
THE ACTIVE SITE CONTAINS TWO METALS: NI AND (PROBABLY) FE. THE LATTER ASSIGNMENT HAS BEEN CONFIRMED BY AN ANOMALOUS DIFFERENCE MAP AND BY A METAL ANALYSIS. THE PUTATIVE FE HAS 3 NON-PROTEIN LIGANDS (L) OF YET UNKNOWN IDENTITY. THESE LIGANDS WERE MODELED AS WATER DURING REFINEMENT. THE USED CRYSTALS MOST LIKELY CONTAIN A MIXTURE OF SEVERAL ACTIVE SITE REDOX STATES (SEE NATURE PUBLICATION). THE ACTUAL OXIDATION STATE OF THE NI AND PUTATIVE FE IN EACH OF THESE STATES IS STILL A MATTER OF INVESTIGATION. THE RESIDUES OF THE ACTIVE SITE ARE LISTED IN THE *SITE* RECORDS BELOW.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (B:43-68,D:43-68)
2: NI_HGENASE_L_2 (B:527-536,D:527-536)
;
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_DESGI
43-68
2
B:43-68
D:43-68
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESGI
527-536
2
B:527-536
D:527-536
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1frva_ (A:)
1b: SCOP_d1frvc_ (C:)
2a: SCOP_d1frvb_ (B:)
2b: SCOP_d1frvd_ (D:)
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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
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
Nickel-iron hydrogenase, small subunit
(16)
Desulfovibrio gigas [TaxId: 879]
(2)
1a
d1frva_
A:
1b
d1frvc_
C:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
Nickel-iron hydrogenase, large subunit
(17)
Desulfovibrio gigas [TaxId: 879]
(3)
2a
d1frvb_
B:
2b
d1frvd_
D:
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1frvA01 (A:3-179)
1b: CATH_1frvC01 (C:3-179)
2a: CATH_1frvA02 (A:180-264)
2b: CATH_1frvC02 (C:180-264)
3a: CATH_1frvB00 (B:7-536)
3b: CATH_1frvD00 (D:7-536)
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)
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 gigas. Organism_taxid: 879.
(2)
1a
1frvA01
A:3-179
1b
1frvC01
C:3-179
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 gigas. Organism_taxid: 879.
(2)
2a
1frvA02
A:180-264
2b
1frvC02
C:180-264
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio gigas. Organism_taxid: 879.
(2)
3a
1frvB00
B:7-536
3b
1frvD00
D:7-536
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Pfam Domains
(0, 0)
Info
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