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1RQK
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (153 KB)
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(1)
Title
:
STRUCTURE OF THE REACTION CENTRE FROM RHODOBACTER SPHAEROIDES CAROTENOIDLESS STRAIN R-26.1 RECONSTITUTED WITH 3,4-DIHYDROSPHEROIDENE
Authors
:
A. W. Roszak, H. Hashimoto, A. T. Gardiner, R. J. Cogdell, N. W. Isaacs
Date
:
05 Dec 03 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Photosynthesis, Photosynthetic Reaction Center, Reconstituted Carotenoid, Carotenoid Binding Site, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. W. Roszak, K. Mckendrick, A. T. Gardiner, I. A. Mitchell, N. W. Isaacs, R. J. Cogdell, H. Hashimoto, H. A. Frank
Protein Regulation Of Carotenoid Binding: Gatekeeper And Locking Amino Acid Residues In Reaction Centers Of Rhodobacter Sphaeroides
Structure V. 12 765 2004
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Hetero Components
(7, 18)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
3a: CARDIOLIPIN (CDLa)
4a: FE (III) ION (FEa)
5a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
5b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
5c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
5d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
5e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
5f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
5g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
6a: 3,4-DIHYDROSPHEROIDENE (SP2a)
7a: UBIQUINONE-10 (U10a)
7b: UBIQUINONE-10 (U10b)
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
LDA
7
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
6
SP2
1
Ligand/Ion
3,4-DIHYDROSPHEROIDENE
7
U10
2
Ligand/Ion
UBIQUINONE-10
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M 500
02
AC2
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:302 , HOH L:910 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BPH M:401 , BCL M:502 , SP2 M:600
BINDING SITE FOR RESIDUE BCL M 501
03
AC3
SOFTWARE
PHE L:97 , ALA L:124 , ILE L:125 , ALA L:127 , TYR L:128 , LEU L:131 , VAL L:157 , ASN L:166 , HIS L:168 , HIS L:173 , ILE L:177 , SER L:244 , CYS L:247 , MET L:248 , BCL L:304 , BPH L:402 , TYR M:210 , BCL M:501 , BCL M:502
BINDING SITE FOR RESIDUE BCL L 302
04
AC4
SOFTWARE
VAL L:157 , TYR L:162 , BCL L:302 , ALA M:153 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , BPH M:401 , BCL M:501 , LDA M:906
BINDING SITE FOR RESIDUE BCL M 502
05
AC5
SOFTWARE
ILE L:46 , TYR L:128 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:302 , BPH L:402 , HOH L:916 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LDA M:902
BINDING SITE FOR RESIDUE BCL L 304
06
AC6
SOFTWARE
PHE L:181 , LEU L:189 , GLY M:63 , LEU M:64 , PHE M:67 , ALA M:125 , TRP M:129 , ALA M:149 , PHE M:150 , ALA M:153 , ALA M:273 , THR M:277 , BCL M:501 , BCL M:502
BINDING SITE FOR RESIDUE BPH M 401
07
AC7
SOFTWARE
PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , TYR L:148 , HIS L:153 , LEU L:238 , VAL L:241 , BCL L:302 , BCL L:304 , LDA L:904 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH L 402
08
AC8
SOFTWARE
THR L:38 , TRP L:100 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , MET M:262 , ILE M:265 , TRP M:268
BINDING SITE FOR RESIDUE U10 M 503
09
AC9
SOFTWARE
PHE L:123 , LEU L:189 , HIS L:190 , LEU L:193 , VAL L:194 , GLU L:212 , ASP L:213 , PHE L:216 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , LEU L:235 , SER L:239 , PHE L:242 , TRP M:41 , LDA M:905
BINDING SITE FOR RESIDUE U10 L 502
10
BC1
SOFTWARE
PHE M:67 , ILE M:70 , TRP M:75 , SER M:119 , TRP M:157 , GLY M:178 , ILE M:179 , HIS M:182 , BCL M:501 , HOH M:931
BINDING SITE FOR RESIDUE SP2 M 600
11
BC2
SOFTWARE
ILE H:22 , TYR H:30 , ASN L:199 , PRO L:200 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , TRP M:155 , ARG M:267 , LEU M:278 , HOH M:934 , HOH M:944
BINDING SITE FOR RESIDUE CDL M 800
12
BC3
SOFTWARE
GLN H:32 , TYR H:40 , ARG M:253 , LDA M:903
BINDING SITE FOR RESIDUE LDA H 901
13
BC4
SOFTWARE
HOH H:958 , BCL L:304 , PRO M:200
BINDING SITE FOR RESIDUE LDA M 902
14
BC5
SOFTWARE
LDA H:901 , PRO L:28 , MET M:256 , GLY M:257
BINDING SITE FOR RESIDUE LDA M 903
15
BC6
SOFTWARE
ILE L:49 , BPH L:402
BINDING SITE FOR RESIDUE LDA L 904
16
BC7
SOFTWARE
VAL L:220 , U10 L:502 , LDA M:906
BINDING SITE FOR RESIDUE LDA M 905
17
BC8
SOFTWARE
BCL M:502 , LDA M:905
BINDING SITE FOR RESIDUE LDA M 906
18
BC9
SOFTWARE
TYR L:115
BINDING SITE FOR RESIDUE LDA L 908
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1rqkh1 (H:36-250)
2a: SCOP_d1rqkl_ (L:)
3a: SCOP_d1rqkm_ (M:)
4a: SCOP_d1rqkh2 (H:10-35)
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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
d1rqkh1
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
:
L (light) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
2a
d1rqkl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1rqkm_
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)
4a
d1rqkh2
H:10-35
[
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]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1rqkH02 (H:117-247)
2a: CATH_1rqkH01 (H:12-116)
3a: CATH_1rqkM01 (M:1-143)
3b: CATH_1rqkL02 (L:164-263)
3c: CATH_1rqkM02 (M:144-302)
3d: CATH_1rqkL01 (L:1-163)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
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: r-26.1.
(3)
1a
1rqkH02
H:117-247
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: r-26.1.
(3)
2a
1rqkH01
H:12-116
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: r-26.1.
(3)
3a
1rqkM01
M:1-143
3b
1rqkL02
L:164-263
3c
1rqkM02
M:144-302
3d
1rqkL01
L:1-163
[
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]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_1rqkH01 (H:141-212)
2a: PFAM_PRCH_1rqkH02 (H:10-137)
3a: PFAM_Photo_RC_1rqkL01 (L:29-272)
3b: PFAM_Photo_RC_1rqkM01 (M:50-302)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1rqkH01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1rqkH02
H:10-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1rqkL01
L:29-272
3b
Photo_RC-1rqkM01
M:50-302
[
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Asymmetric Unit 1
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