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1YF6
Asym. Unit
Info
Asym.Unit (162 KB)
Biol.Unit 1 (152 KB)
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(1)
Title
:
STRUCTURE OF A QUINTUPLE MUTANT OF PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES
Authors
:
M. L. Paddock, C. Chang, Q. Xu, E. C. Abresch, H. L. Axelrod
Date
:
30 Dec 04 (Deposition) - 17 May 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Bacterial Photosynthesis, Rhodobacter Sphaeroides, Gated Electron Transfer, Quinone Movement, Integral Membrane Protein, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. L. Paddock, C. Chang, Q. Xu, E. C. Abresch, H. L. Axelrod, G. Feher, M. Y. Okamura
Quinone (Q(B)) Reduction By B-Branch Electron Transfer In Mutant Bacterial Reaction Centers From Rhodobacter Sphaeroides: Quantum Efficiency And X-Ray Structure.
Biochemistry V. 44 6920 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(11, 20)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL A (BCLa)
01b: BACTERIOCHLOROPHYLL A (BCLb)
01c: BACTERIOCHLOROPHYLL A (BCLc)
01d: BACTERIOCHLOROPHYLL A (BCLd)
01e: BACTERIOCHLOROPHYLL A (BCLe)
02a: BACTERIOPHEOPHYTIN A (BPHa)
03a: CARDIOLIPIN (CDLa)
04a: CHLORIDE ION (CLa)
05a: FE (II) ION (FE2a)
06a: GLYCEROL (GOLa)
07a: HEPTANE-1,2,3-TRIOL (HTOa)
08a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
08b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
08c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
09a: PHOSPHATE ION (PO4a)
09b: PHOSPHATE ION (PO4b)
10a: SPHEROIDENE (SPOa)
11a: UBIQUINONE-10 (U10a)
11b: UBIQUINONE-10 (U10b)
11c: UBIQUINONE-10 (U10c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
5
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
1
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
CDL
1
Ligand/Ion
CARDIOLIPIN
4
CL
1
Ligand/Ion
CHLORIDE ION
5
FE2
1
Ligand/Ion
FE (II) ION
6
GOL
1
Ligand/Ion
GLYCEROL
7
HTO
1
Ligand/Ion
HEPTANE-1,2,3-TRIOL
8
LDA
3
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
9
PO4
2
Ligand/Ion
PHOSPHATE ION
10
SPO
1
Ligand/Ion
SPHEROIDENE
11
U10
3
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(20, 20)
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)
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 FE2 M 850
02
AC2
SOFTWARE
HIS M:219 , THR M:222 , TRP M:260 , ILE M:265
BINDING SITE FOR RESIDUE CL M 861
03
AC3
SOFTWARE
ASN M:28 , GLY M:53 , SER M:54 , HOH M:1189 , HOH M:1193 , HOH M:1215
BINDING SITE FOR RESIDUE PO4 M 867
04
AC4
SOFTWARE
HIS H:126 , GLU L:72 , TYR L:73 , LYS L:82 , THR M:21 , HOH M:1101 , HOH M:1330
BINDING SITE FOR RESIDUE PO4 M 868
05
AC5
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , TYR L:181 , THR L:182 , BPH L:855 , HOH L:1011 , MET M:122 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:853 , SPO M:860
BINDING SITE FOR RESIDUE BCL M 851
06
AC6
SOFTWARE
ALA L:124 , ALA L:127 , TRP L:156 , VAL L:157 , THR L:160 , ASN L:166 , PHE L:167 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , TYR L:181 , SER L:244 , CYS L:247 , MET L:248 , BCL L:854 , PHE M:210 , BCL M:853 , BCL M:856
BINDING SITE FOR RESIDUE BCL L 852
07
AC7
SOFTWARE
VAL L:157 , TYR L:162 , BCL L:852 , BPH L:855 , MET M:122 , ALA M:153 , LEU M:156 , TRP M:157 , LEU M:160 , THR M:186 , ASN M:187 , SER M:190 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , VAL M:276 , GLY M:280 , ILE M:284 , BCL M:851
BINDING SITE FOR RESIDUE BCL M 853
08
AC8
SOFTWARE
TYR L:128 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:852 , LDA L:864 , PHE M:197 , ASP M:203 , ILE M:206 , ALA M:207 , PHE M:210 , BCL M:856
BINDING SITE FOR RESIDUE BCL L 854
09
AC9
SOFTWARE
TYR L:181 , ALA L:184 , LEU L:185 , LEU L:189 , SER M:59 , LEU M:60 , GLY M:63 , VAL M:126 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:851 , BCL M:853
BINDING SITE FOR RESIDUE BPH L 855
10
BC1
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 , VAL L:241 , BCL L:852 , BCL L:854 , PHE M:210 , ALA M:213 , HIS M:214 , TRP M:252 , MET M:256 , PHE M:258
BINDING SITE FOR RESIDUE BCL M 856
11
BC2
SOFTWARE
GLN H:32 , HOH H:1032 , PHE M:258 , ASN M:259 , TRP M:260 , TRP M:268
BINDING SITE FOR RESIDUE U10 M 857
12
BC3
SOFTWARE
ALA L:186 , LEU L:189 , HIS L:190 , LEU L:193 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229 , HOH L:1074
BINDING SITE FOR RESIDUE U10 L 858
13
BC4
SOFTWARE
TRP L:263 , TRP L:265 , TRP L:266 , LEU M:86 , PHE M:90 , HOH M:1111
BINDING SITE FOR RESIDUE U10 L 859
14
BC5
SOFTWARE
PHE M:67 , ILE M:70 , GLY M:71 , TRP M:75 , SER M:119 , TRP M:157 , GLY M:161 , GLY M:178 , HIS M:182 , BCL M:851
BINDING SITE FOR RESIDUE SPO M 860
15
BC6
SOFTWARE
TYR H:30 , ASN L:199 , PRO L:200 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , ARG M:267 , ILE M:270 , LEU M:278 , HOH M:1155 , HOH M:1234 , HOH M:1247 , HOH M:1270
BINDING SITE FOR RESIDUE CDL M 862
16
BC7
SOFTWARE
PRO L:118 , PHE L:119
BINDING SITE FOR RESIDUE HTO L 863
17
BC8
SOFTWARE
TRP L:151 , BCL L:854 , PRO M:200 , ASP M:203 , PHE M:208
BINDING SITE FOR RESIDUE LDA L 864
18
BC9
SOFTWARE
LEU L:75 , GLY L:76 , GLY L:77 , GLN L:87 , ILE L:91 , TRP L:142
BINDING SITE FOR RESIDUE LDA L 865
19
CC1
SOFTWARE
PHE M:105 , ALA M:107 , LEU M:109
BINDING SITE FOR RESIDUE LDA M 866
20
CC2
SOFTWARE
GLU H:43 , GLY H:47 , HOH H:1009 , ARG L:7 , HOH L:1045 , HOH L:1184 , HOH L:1239
BINDING SITE FOR RESIDUE GOL L 869
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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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Label:
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_d1yf6h2 (H:36-248)
2a: SCOP_d1yf6l_ (L:)
3a: SCOP_d1yf6m_ (M:)
4a: SCOP_d1yf6h1 (H:11-35)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d1yf6h2
H:36-248
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
d1yf6l_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1yf6m_
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
d1yf6h1
H:11-35
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1yf6H02 (H:117-248)
2a: CATH_1yf6H01 (H:12-116)
3a: CATH_1yf6M01 (M:1-143)
3b: CATH_1yf6M02 (M:144-301)
3c: CATH_1yf6L01 (L:1-163)
3d: CATH_1yf6L02 (L:164-263)
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)
Topologies
(
)
(
)
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.
(12)
1a
1yf6H02
H:117-248
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.
(12)
2a
1yf6H01
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.
(12)
3a
1yf6M01
M:1-143
3b
1yf6M02
M:144-301
3c
1yf6L01
L:1-163
3d
1yf6L02
L:164-263
[
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]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_1yf6H01 (H:141-212)
2a: PFAM_PRCH_1yf6H02 (H:11-137)
3a: PFAM_Photo_RC_1yf6L01 (L:29-272)
3b: PFAM_Photo_RC_1yf6M01 (M:50-301)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1yf6H01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1yf6H02
H:11-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1yf6L01
L:29-272
3b
Photo_RC-1yf6M01
M:50-301
[
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