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Asym. Unit
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Asym.Unit (168 KB)
Biol.Unit 1 (155 KB)
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(1)
Title
:
HEXA-COORDINATION OF A BACTERIOCHLOROPHYLL COFACTOR IN THE RHODOBACTER SPHAEROIDES REACTION CENTRE
Authors
:
M. Marsh, D. Frolov, L. I. Crouch, P. K. Fyfe, B. Robert, R. Vangrondelle, M. R. Jones, A. T. Hadfield
Date
:
02 Nov 09 (Deposition) - 09 Feb 10 (Release) - 26 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.63
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Photosynthesis, Reaction Center, Membrane Protein, Photosynthetic Reaction Center, Electron Transport, Bacteriochlorophyll, Iron, Membrane, Magnesium, Transport, Chromophore, Chlorophyll, Metal-Binding, Transmembrane
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Frolov, M. Marsh, L. I. Crouch, P. K. Fyfe, B. Robert, R. Vangrondelle, A. T. Hadfield, M. R. Jones
Structural And Spectroscopic Consequences Of Hexa- Coordination Of A Bacteriochlorophyll Cofactor In The Rhodobacter Sphaeroides Reaction Centre
Biochemistry V. 49 1882 2010
[
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Hetero Components
(10, 23)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL A (BCLa)
01b: BACTERIOCHLOROPHYLL A (BCLb)
01c: BACTERIOCHLOROPHYLL A (BCLc)
01d: BACTERIOCHLOROPHYLL A (BCLd)
02a: BACTERIOPHEOPHYTIN A (BPHa)
02b: BACTERIOPHEOPHYTIN A (BPHb)
03a: CARDIOLIPIN (CDLa)
04a: FE (III) ION (FEa)
05a: GLYCEROL (GOLa)
05b: GLYCEROL (GOLb)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
06b: HEPTANE-1,2,3-TRIOL (HTOb)
06c: HEPTANE-1,2,3-TRIOL (HTOc)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
07c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
07d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
07e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
07f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
08a: SODIUM ION (NAa)
08b: SODIUM ION (NAb)
09a: SPEROIDENONE (SPNa)
10a: UBIQUINONE-10 (U10a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
2
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CDL
1
Ligand/Ion
CARDIOLIPIN
4
FE
1
Ligand/Ion
FE (III) ION
5
GOL
2
Ligand/Ion
GLYCEROL
6
HTO
3
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
LDA
6
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
NA
2
Ligand/Ion
SODIUM ION
9
SPN
1
Ligand/Ion
SPEROIDENONE
10
U10
1
Ligand/Ion
UBIQUINONE-10
[
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]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , ARG L:181 , THR L:182 , BCL L:1283 , HOH L:2073 , HOH L:2097 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1303 , BPH M:1314 , SPN M:1315
BINDING SITE FOR RESIDUE BCL L1282
02
AC2
SOFTWARE
PHE L:97 , ALA L:124 , ALA L:127 , VAL L:157 , TYR L:162 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , CYS L:247 , MET L:248 , BCL L:1282 , BPH L:1288 , TYR M:210 , BCL M:1303 , BCL M:1304
BINDING SITE FOR RESIDUE BCL L1283
03
AC3
SOFTWARE
VAL L:157 , TYR L:162 , ARG L:181 , BCL L:1282 , BCL L:1283 , LEU M:156 , THR M:186 , ASN M:187 , LEU M:196 , PHE M:197 , HIS M:202 , ILE M:206 , LEU M:209 , TYR M:210 , GLY M:280 , ILE M:284 , BCL M:1304 , BPH M:1314
BINDING SITE FOR RESIDUE BCL M1303
04
AC4
SOFTWARE
TYR L:128 , HIS L:153 , LEU L:154 , BCL L:1283 , BPH L:1288 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BCL M:1303 , LDA M:1306 , HOH M:2081
BINDING SITE FOR RESIDUE BCL M1304
05
AC5
SOFTWARE
PHE H:23 , LEU H:27 , TYR H:30 , ASN L:199 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , ILE M:270 , TRP M:271 , LEU M:278 , HOH M:2082
BINDING SITE FOR RESIDUE CDL M1305
06
AC6
SOFTWARE
PRO M:200 , LEU M:204 , ALA M:207 , BCL M:1304 , LDA M:1307
BINDING SITE FOR RESIDUE LDA M1306
07
AC7
SOFTWARE
TYR H:40 , PHE H:56 , ARG M:253 , GLY M:257 , PHE M:258 , LDA M:1306 , LDA M:1308 , U10 M:1316
BINDING SITE FOR RESIDUE LDA M1307
08
AC8
SOFTWARE
LDA H:1251 , HOH H:2025 , MET M:256 , GLY M:257 , LDA M:1307
BINDING SITE FOR RESIDUE LDA M1308
09
AC9
SOFTWARE
VAL L:220 , HTO L:1287 , GLY M:31 , VAL M:32
BINDING SITE FOR RESIDUE LDA M1309
10
BC1
SOFTWARE
HTO L:1287 , LEU M:39 , TRP M:41
BINDING SITE FOR RESIDUE LDA M1310
11
BC2
SOFTWARE
TRP H:21 , LDA M:1308
BINDING SITE FOR RESIDUE LDA H1251
12
BC3
SOFTWARE
GLU H:43 , HOH H:2020 , HOH H:2047 , ARG L:7
BINDING SITE FOR RESIDUE GOL L1284
13
BC4
SOFTWARE
TRP L:265
BINDING SITE FOR RESIDUE GOL L1285
14
BC5
SOFTWARE
MET H:134 , ALA H:137 , PHE H:140 , HOH H:2074 , HOH H:2075
BINDING SITE FOR RESIDUE NA H1252
15
BC6
SOFTWARE
ASN M:28 , SER M:54 , HOH M:2025 , HOH M:2026
BINDING SITE FOR RESIDUE NA M1311
16
BC7
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M1312
17
BC8
SOFTWARE
HIS L:190 , LEU L:193 , PHE L:216 , SER L:223 , GLY L:225 , ILE L:229
BINDING SITE FOR RESIDUE HTO L1286
18
BC9
SOFTWARE
TRP L:266 , LEU M:86 , ARG M:87 , LEU M:89 , PHE M:90 , PHE M:91
BINDING SITE FOR RESIDUE HTO M1313
19
CC1
SOFTWARE
VAL L:220 , LDA M:1309 , LDA M:1310
BINDING SITE FOR RESIDUE HTO L1287
20
CC2
SOFTWARE
ARG L:181 , ALA L:184 , LEU L:185 , LEU L:189 , LEU L:219 , BCL L:1282 , LEU M:60 , GLY M:63 , ALA M:125 , VAL M:126 , TRP M:129 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:1303
BINDING SITE FOR RESIDUE BPH M1314
21
CC3
SOFTWARE
ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , ALA L:124 , HIS L:153 , LEU L:238 , BCL L:1283 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256 , BCL M:1304
BINDING SITE FOR RESIDUE BPH L1288
22
CC4
SOFTWARE
BCL L:1282 , PHE M:67 , PHE M:68 , GLY M:71 , TRP M:75 , PHE M:105 , TRP M:115 , SER M:119 , MET M:122 , TRP M:157 , LEU M:160 , GLY M:161 , TRP M:171 , VAL M:175 , GLY M:178 , HIS M:182
BINDING SITE FOR RESIDUE SPN M1315
23
CC5
SOFTWARE
PHE L:29 , TRP L:100 , HOH L:2022 , MET M:218 , HIS M:219 , THR M:222 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , ILE M:265 , TRP M:268 , LDA M:1307
BINDING SITE FOR RESIDUE U10 M1316
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,L:166-192,M:195-221,M:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOS4
167-193
1
L:166-192
RCEL_RHOSH
167-193
1
L:166-192
RCEM_RHOS4
196-222
1
M:195-221
RCEM_RHOSH
196-222
1
M:195-221
[
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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.
SCOP Domains
(3, 4)
Info
All SCOP Domains
1a: SCOP_d2wx5h2 (H:36-250)
2a: SCOP_d2wx5l_ (L:)
2b: SCOP_d2wx5m_ (M:)
3a: SCOP_d2wx5h1 (H:11-35)
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(
)
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Folds
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(
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PRC-barrel domain
(113)
Superfamily
:
PRC-barrel domain
(113)
Family
:
Photosynthetic reaction centre, H-chain, cytoplasmic domain
(108)
Protein domain
:
Photosynthetic reaction centre
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
1a
d2wx5h2
H:36-250
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Superfamily
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Family
:
Bacterial photosystem II reaction centre, L and M subunits
(187)
Protein domain
:
automated matches
(44)
Rhodobacter sphaeroides [TaxId: 1063]
(31)
2a
d2wx5l_
L:
2b
d2wx5m_
M:
Fold
:
Single transmembrane helix
(568)
Superfamily
:
Photosystem II reaction centre subunit H, transmembrane region
(108)
Family
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Protein domain
:
Photosystem II reaction centre subunit H, transmembrane region
(98)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
3a
d2wx5h1
H:11-35
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2wx5H02 (H:117-250)
2a: CATH_2wx5H01 (H:11-116)
3a: CATH_2wx5M01 (M:1-143)
3b: CATH_2wx5L01 (L:1-163)
3c: CATH_2wx5L02 (L:164-263)
3d: CATH_2wx5M02 (M:144-302)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 2
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 2
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: ncib 8253.
(4)
1a
2wx5H02
H:117-250
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Photosynthetic Reaction Center; Chain H, domain 1
(93)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit H, domain 1
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: ncib 8253.
(4)
2a
2wx5H01
H:11-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: ncib 8253.
(4)
3a
2wx5M01
M:1-143
3b
2wx5L01
L:1-163
3c
2wx5L02
L:164-263
3d
2wx5M02
M:144-302
[
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]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_2wx5H01 (H:141-212)
2a: PFAM_PRCH_2wx5H02 (H:11-137)
3a: PFAM_Photo_RC_2wx5L01 (L:29-272)
3b: PFAM_Photo_RC_2wx5M01 (M:50-302)
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Clans
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Families
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(
)
Organisms
(
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(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(1)
1a
PRC-2wx5H01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(1)
2a
PRCH-2wx5H02
H:11-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
(1)
3a
Photo_RC-2wx5L01
L:29-272
3b
Photo_RC-2wx5M01
M:50-302
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Asym.Unit (168 KB)
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