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2V4J
Asym. Unit
Info
Asym.Unit (332 KB)
Biol.Unit 1 (320 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF DESULFOVIBRIO VULGARIS DISSIMILATORY SULFITE REDUCTASE BOUND TO DSRC PROVIDES NOVEL INSIGHTS INTO THE MECHANISM OF SULFATE RESPIRATION
Authors
:
T. F. Oliveira, C. Vonrhein, P. M. Matias, S. S. Venceslau, I. A. C. Pereira, M. Archer
Date
:
22 Sep 08 (Deposition) - 02 Dec 08 (Release) - 16 Jul 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Dissimilatory Sulfite Reductase, Siroheme, Oxidoreductase, Sirohydrochlorin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. F. Oliveira, C. Vonrhein, P. M. Matias, S. S. Venceslau, I. A. C. Pereira, M. Archer
The Crystal Structure Of Desulfovibrio Vulgaris Dissimilatory Sulfite Reductase Bound To Dsrc Provides Novel Insights Into The Mechanism Of Sulfate Respiration.
J. Biol. Chem. V. 283 34141 2008
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(4, 14)
Info
All Hetero Components
1a: IRON/SULFUR CLUSTER (SF4a)
1b: IRON/SULFUR CLUSTER (SF4b)
1c: IRON/SULFUR CLUSTER (SF4c)
1d: IRON/SULFUR CLUSTER (SF4d)
1e: IRON/SULFUR CLUSTER (SF4e)
1f: IRON/SULFUR CLUSTER (SF4f)
1g: IRON/SULFUR CLUSTER (SF4g)
1h: IRON/SULFUR CLUSTER (SF4h)
2a: 3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,... (SH0a)
2b: 3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,... (SH0b)
3a: SULFITE ION (SO3a)
3b: SULFITE ION (SO3b)
4a: SIROHEME (SRMa)
4b: SIROHEME (SRMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SF4
8
Ligand/Ion
IRON/SULFUR CLUSTER
2
SH0
2
Ligand/Ion
3,3',3'',3'''-[(1R,2S,3S,4S,7S,8S,11S,12S,13S,16S,19S)-3,8,13,17-TETRAKIS(CARBOXYLATOMETHYL)-8,13-DIMETHYL-1,2,3,4,7,8,13,16,19,20,22,24-TETRADECAHYDROPORPHYRIN-2,7,12,18-TETRAYL]TETRAPROPANOATE
3
SO3
2
Ligand/Ion
SULFITE ION
4
SRM
2
Ligand/Ion
SIROHEME
[
close Hetero Component info
]
Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:177 , CYS A:183 , PHE A:185 , ALA A:186 , ALA A:220 , CYS A:221 , ASN A:223 , CYS A:225 , SH0 A:503
BINDING SITE FOR RESIDUE SF4 A 501
02
AC2
SOFTWARE
CYS A:284 , CYS A:288 , CYS A:303 , VAL A:304 , ARG A:305 , CYS A:306 , MET A:307 , CYS A:309
BINDING SITE FOR RESIDUE SF4 A 502
03
AC3
SOFTWARE
CYS A:177 , LEU A:178 , ARG A:182 , CYS A:183 , GLU A:184 , PHE A:185 , ASN A:223 , GLY A:224 , CYS A:225 , ASN A:262 , ASN A:311 , SF4 A:501 , HOH A:2135 , HOH A:2161 , HOH A:2303 , HOH A:2304 , HOH A:2305 , HOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309 , HOH A:2310 , HOH A:2311 , HOH A:2312 , HIS B:44 , HIS B:54 , ARG B:66 , ARG B:94 , THR B:96 , THR B:97 , ARG B:98 , ASN B:100 , GLU B:102 , GLY B:134 , GLY B:136 , SER B:140 , ARG B:183 , LYS B:288 , VAL B:289 , SER B:290 , ARG B:292 , ARG B:336 , HOH B:2210
BINDING SITE FOR RESIDUE SH0 A 503
04
AC4
SOFTWARE
CYS B:151 , THR B:153 , PRO B:154 , CYS B:188 , CYS B:189 , ASN B:191 , CYS B:193 , SRM B:503
BINDING SITE FOR RESIDUE SF4 B 501
05
AC5
SOFTWARE
CYS B:231 , VAL B:236 , CYS B:258 , MET B:259 , CYS B:261 , GLY B:262 , CYS B:264
BINDING SITE FOR RESIDUE SF4 B 502
06
AC6
SOFTWARE
ILE A:81 , ARG A:83 , ARG A:101 , GLY A:134 , SER A:135 , THR A:136 , GLY A:137 , ASP A:138 , TYR A:212 , LYS A:213 , LYS A:215 , LYS A:217 , ARG A:231 , LYS A:332 , ALA A:333 , ILE A:335 , ARG A:376 , ARG A:378 , HOH A:2079 , HOH A:2103 , ARG B:71 , THR B:145 , GLN B:146 , HIS B:150 , HIS B:152 , ASN B:191 , CYS B:193 , GLY B:194 , SF4 B:501 , SO3 B:504 , HOH B:2150 , HOH B:2273 , HOH B:2274 , GLY C:103 , CYS C:104
BINDING SITE FOR RESIDUE SRM B 503
07
AC7
SOFTWARE
ARG A:101 , ARG A:172 , LYS A:213 , LYS A:215 , SRM B:503 , CYS C:104 , HOH C:2058
BINDING SITE FOR RESIDUE SO3 B 504
08
AC8
SOFTWARE
CYS D:177 , CYS D:183 , PHE D:185 , ALA D:186 , ALA D:220 , CYS D:221 , ASN D:223 , CYS D:225
BINDING SITE FOR RESIDUE SF4 D 501
09
AC9
SOFTWARE
CYS D:284 , CYS D:288 , CYS D:303 , VAL D:304 , ARG D:305 , CYS D:306 , MET D:307 , CYS D:309
BINDING SITE FOR RESIDUE SF4 D 502
10
BC1
SOFTWARE
CYS D:177 , LEU D:178 , ARG D:182 , CYS D:183 , GLU D:184 , PHE D:185 , ASN D:223 , GLY D:224 , CYS D:225 , ASN D:262 , ASN D:311 , HOH D:2052 , HOH D:2173 , HOH D:2174 , HOH D:2175 , HOH D:2176 , HOH D:2177 , HOH D:2178 , HOH D:2179 , HOH D:2180 , HOH D:2181 , HIS E:44 , HIS E:54 , ARG E:66 , ARG E:94 , THR E:96 , THR E:97 , ARG E:98 , ASN E:100 , GLU E:102 , GLY E:134 , GLY E:136 , SER E:140 , ARG E:183 , VAL E:289 , SER E:290 , ARG E:292 , ARG E:336
BINDING SITE FOR RESIDUE SH0 D 503
11
BC2
SOFTWARE
CYS E:151 , THR E:153 , PRO E:154 , CYS E:188 , CYS E:189 , ASN E:191 , CYS E:193 , SRM E:503
BINDING SITE FOR RESIDUE SF4 E 501
12
BC3
SOFTWARE
CYS E:231 , THR E:233 , VAL E:236 , CYS E:258 , MET E:259 , CYS E:261 , GLY E:262 , CYS E:264
BINDING SITE FOR RESIDUE SF4 E 502
13
BC4
SOFTWARE
ILE D:81 , ARG D:83 , ARG D:101 , GLY D:134 , SER D:135 , THR D:136 , GLY D:137 , ASP D:138 , TYR D:212 , LYS D:213 , LYS D:215 , LYS D:217 , ARG D:231 , ALA D:333 , ILE D:335 , ARG D:376 , ARG D:378 , ARG E:71 , THR E:145 , GLN E:146 , HIS E:150 , HIS E:152 , ASN E:191 , CYS E:193 , GLY E:194 , SF4 E:501 , SO3 E:504 , HOH E:2053 , HOH E:2164 , GLY F:103 , CYS F:104
BINDING SITE FOR RESIDUE SRM E 503
14
BC5
SOFTWARE
ARG D:101 , ARG D:172 , LYS D:213 , LYS D:215 , SRM E:503 , CYS F:104
BINDING SITE FOR RESIDUE SO3 E 504
[
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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, 6)
Info
All PROSITE Patterns/Profiles
1: 4FE4S_FER_2 (B:249-276,E:249-276,A:294-322,D:29...)
2: 4FE4S_FER_1 (B:258-269,E:258-269)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
4FE4S_FER_2
PS51379
4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
DSVB_DESVH
249-276
2
B:249-276
E:249-276
DSVA_DESVH
294-322
2
A:294-322
D:294-322
2
4FE4S_FER_1
PS00198
4Fe-4S ferredoxin-type iron-sulfur binding region signature.
DSVB_DESVH
258-269
2
B:258-269
E:258-269
[
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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.
SCOP Domains
(8, 14)
Info
All SCOP Domains
1a: SCOP_d2v4jf_ (F:)
2a: SCOP_d2v4jc1 (C:3-105)
3a: SCOP_d2v4ja1 (A:242-322)
3b: SCOP_d2v4jd1 (D:242-322)
4a: SCOP_d2v4jb1 (B:209-277)
4b: SCOP_d2v4je1 (E:209-277)
5a: SCOP_d2v4ja2 (A:2-167)
5b: SCOP_d2v4jd2 (D:2-167)
6a: SCOP_d2v4jb2 (B:2-135)
6b: SCOP_d2v4je2 (E:2-135)
7a: SCOP_d2v4ja3 (A:168-241,A:323-437)
7b: SCOP_d2v4jd3 (D:168-241,D:323-437)
8a: SCOP_d2v4jb3 (B:136-208,B:278-381)
8b: SCOP_d2v4je3 (E:136-208,E:278-381)
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)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
DsrC, the gamma subunit of dissimilatory sulfite reductase
(9)
Superfamily
:
DsrC, the gamma subunit of dissimilatory sulfite reductase
(9)
Family
:
automated matches
(1)
Protein domain
:
automated matches
(1)
Desulfovibrio vulgaris [TaxId: 882]
(1)
1a
d2v4jf_
F:
Family
:
DsrC, the gamma subunit of dissimilatory sulfite reductase
(8)
Protein domain
:
DsrC, the gamma subunit of dissimilatory sulfite reductase
(5)
Desulfovibrio vulgaris [TaxId: 881]
(1)
2a
d2v4jc1
C:3-105
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
4Fe-4S ferredoxins
(143)
Family
:
Ferredoxin domains from multidomain proteins
(69)
Protein domain
:
DsrA insert domain
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
3a
d2v4ja1
A:242-322
3b
d2v4jd1
D:242-322
Protein domain
:
DsrB insert domain
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
4a
d2v4jb1
B:209-277
4b
d2v4je1
E:209-277
Superfamily
:
Nitrite/Sulfite reductase N-terminal domain-like
(52)
Family
:
DsrA/DsrB N-terminal-domain-like
(18)
Protein domain
:
Dissimilatory sulfite reductase subunit alpha, DsrA
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
5a
d2v4ja2
A:2-167
5b
d2v4jd2
D:2-167
Protein domain
:
Dissimilatory sulfite reductase subunit beta, DsrB
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
6a
d2v4jb2
B:2-135
6b
d2v4je2
E:2-135
Fold
:
Nitrite and sulphite reductase 4Fe-4S domain-like
(52)
Superfamily
:
Nitrite and sulphite reductase 4Fe-4S domain-like
(52)
Family
:
Nitrite and sulphite reductase 4Fe-4S domain-like
(33)
Protein domain
:
Dissimilatory sulfite reductase subunit alpha, DsrA
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
7a
d2v4ja3
A:168-241,A:323-437
7b
d2v4jd3
D:168-241,D:323-437
Protein domain
:
Dissimilatory sulfite reductase subunit beta, DsrB
(9)
Desulfovibrio vulgaris [TaxId: 881]
(1)
8a
d2v4jb3
B:136-208,B:278-381
8b
d2v4je3
E:136-208,E:278-381
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2v4jC01 (C:3-41)
1b: CATH_2v4jF01 (F:3-41)
2a: CATH_2v4jC02 (C:42-105)
2b: CATH_2v4jF02 (F:42-105)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Dissimilatory Siroheme-sulfite Reductase; Chain: A; domain 1
(4)
Homologous Superfamily
:
[code=3.30.1420.10, no name defined]
(4)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
1a
2v4jC01
C:3-41
1b
2v4jF01
F:3-41
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
[code=1.10.10.370, no name defined]
(5)
Desulfovibrio vulgaris. Organism_taxid: 882. Strain: hildenborough.
(1)
2a
2v4jC02
C:42-105
2b
2v4jF02
F:42-105
[
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Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_DsrC_2v4jF01 (F:3-105)
1b: PFAM_DsrC_2v4jF02 (F:3-105)
2a: PFAM_NIR_SIR_2v4jD01 (D:167-404)
2b: PFAM_NIR_SIR_2v4jD02 (D:167-404)
2c: PFAM_NIR_SIR_2v4jE01 (E:135-361)
2d: PFAM_NIR_SIR_2v4jE02 (E:135-361)
3a: PFAM_NIR_SIR_ferr_2v4jD03 (D:91-158)
3b: PFAM_NIR_SIR_ferr_2v4jD04 (D:91-158)
3c: PFAM_NIR_SIR_ferr_2v4jE03 (E:54-121)
3d: PFAM_NIR_SIR_ferr_2v4jE04 (E:54-121)
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)
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(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: DsrC]
(2)
Family
:
DsrC
(2)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
1a
DsrC-2v4jF01
F:3-105
1b
DsrC-2v4jF02
F:3-105
Clan
:
no clan defined [family: NIR_SIR]
(11)
Family
:
NIR_SIR
(11)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
2a
NIR_SIR-2v4jD01
D:167-404
2b
NIR_SIR-2v4jD02
D:167-404
2c
NIR_SIR-2v4jE01
E:135-361
2d
NIR_SIR-2v4jE02
E:135-361
Clan
:
no clan defined [family: NIR_SIR_ferr]
(11)
Family
:
NIR_SIR_ferr
(11)
Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)
(1)
3a
NIR_SIR_ferr-2v4jD03
D:91-158
3b
NIR_SIR_ferr-2v4jD04
D:91-158
3c
NIR_SIR_ferr-2v4jE03
E:54-121
3d
NIR_SIR_ferr-2v4jE04
E:54-121
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