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2JIY
Asym. Unit
Info
Asym.Unit (167 KB)
Biol.Unit 1 (154 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH TRP (CHAIN M, AM149W)
Authors
:
P. K. Fyfe, J. A. Potter, J. Cheng, C. M. Williams, A. J. Watson, M. R. Jon
Date
:
03 Jul 07 (Deposition) - 04 Sep 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : H,L,M
Biol. Unit 1: H,L,M (1x)
Keywords
:
Photosynthesis, Membrane Protein, Electron Transport, Bacteriochlorophyll, Chlorophyll, Metal-Binding, Transport, Chromophore
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. K. Fyfe, J. A. Potter, J. Cheng, C. M. Williams, A. J. Watson, M. R. Jones
Structural Responses To Cavity-Creating Mutations In An Integral Membrane Protein.
Biochemistry V. 46 10461 2007
(for further references see the
PDB file header
)
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Hetero Components
(10, 15)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL A (BCLa)
01b: BACTERIOCHLOROPHYLL A (BCLb)
01c: BACTERIOCHLOROPHYLL A (BCLc)
01d: BACTERIOCHLOROPHYLL A (BCLd)
02a: BACTERIOPHEOPHYTIN A (BPHa)
03a: CARDIOLIPIN (CDLa)
04a: CHLORIDE ION (CLa)
05a: DODECANE (D12a)
06a: FE (III) ION (FEa)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
08a: PHOSPHATE ION (PO4a)
09a: SPEROIDENONE (SPNa)
10a: UBIQUINONE-10 (U10a)
10b: UBIQUINONE-10 (U10b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
4
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
D12
1
Ligand/Ion
DODECANE
6
FE
1
Ligand/Ion
FE (III) ION
7
LDA
2
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
PO4
1
Ligand/Ion
PHOSPHATE ION
9
SPN
1
Ligand/Ion
SPEROIDENONE
10
U10
2
Ligand/Ion
UBIQUINONE-10
[
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Sites
(15, 15)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BCL L:1283 , HOH L:2055 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1303 , SPN M:1309
BINDING SITE FOR RESIDUE BCL L1282
02
AC2
SOFTWARE
ALA L:124 , ALA L:127 , LEU L:131 , VAL L:157 , SER L:158 , 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 , BCL L:1284 , BPH L:1285 , BCL M:1303 , U10 M:1310
BINDING SITE FOR RESIDUE BCL L1283
03
AC3
SOFTWARE
VAL L:157 , TYR L:162 , PHE L:181 , BCL L:1282 , BCL L:1283 , TRP M:66 , ALA M:153 , LEU M:156 , LEU M:160 , THR M:186 , ASN M:187 , PHE M:189 , LEU M:196 , PHE M:197 , HIS M:202 , SER M:205 , ILE M:206 , LEU M:209 , TYR M:210 , VAL M:276 , GLY M:280 , ILE M:284 , SPN M:1309
BINDING SITE FOR RESIDUE BCL M1303
04
AC4
SOFTWARE
TYR L:128 , LEU L:131 , PHE L:146 , ILE L:150 , TRP L:151 , HIS L:153 , LEU L:154 , BCL L:1283 , BPH L:1285 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , LDA M:1305 , HOH M:2083
BINDING SITE FOR RESIDUE BCL L1284
05
AC5
SOFTWARE
ALA H:16 , TYR H:30 , HOH H:2003 , ASN L:199 , PRO L:200 , GLY M:143 , LYS M:144 , HIS M:145 , TRP M:148 , TRP M:155 , ARG M:267 , HOH M:2121
BINDING SITE FOR RESIDUE CDL M1304
06
AC6
SOFTWARE
GLN H:32 , TYR H:40 , GLY H:54 , HOH H:2036 , ARG M:253 , PHE M:258 , LDA M:1305
BINDING SITE FOR RESIDUE LDA H1251
07
AC7
SOFTWARE
LDA H:1251 , BCL L:1284 , PRO M:200 , LEU M:204 , ALA M:207
BINDING SITE FOR RESIDUE LDA M1305
08
AC8
SOFTWARE
TRP M:129
BINDING SITE FOR RESIDUE CL M1311
09
AC9
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE M1306
10
BC1
SOFTWARE
ASN M:28 , GLY M:53 , SER M:54 , HOH M:2122 , HOH M:2123
BINDING SITE FOR RESIDUE PO4 M1307
11
BC2
SOFTWARE
THR L:38 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , PHE L:123 , ALA L:124 , VAL L:241 , BCL L:1283 , BCL L:1284 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH L1285
12
BC3
SOFTWARE
BCL L:1282 , PHE M:67 , PHE M:68 , ILE M:70 , GLY M:71 , PHE M:74 , TRP M:75 , SER M:119 , TRP M:157 , GLY M:161 , TRP M:171 , HIS M:182 , BCL M:1303
BINDING SITE FOR RESIDUE SPN M1309
13
BC4
SOFTWARE
PHE L:29 , TYR L:30 , BCL L:1283 , MET M:218 , HIS M:219 , THR M:222 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , ILE M:265 , TRP M:268
BINDING SITE FOR RESIDUE U10 M1310
14
BC5
SOFTWARE
THR L:182 , LEU L:189 , HIS L:190 , LEU L:193 , 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
BINDING SITE FOR RESIDUE U10 L1286
15
BC6
SOFTWARE
MET M:256 , GLY M:257
BINDING SITE FOR RESIDUE D12 M1314
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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
(1, 2)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,M:195-221)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_RHOSH
167-193
1
L:166-192
RCEM_RHOSH
196-222
1
M:195-221
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Exons
(0, 0)
Info
All Exons
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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_d2jiyh2 (H:36-250)
2a: SCOP_d2jiyl_ (L:)
2b: SCOP_d2jiym_ (M:)
3a: SCOP_d2jiyh1 (H:11-35)
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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
d2jiyh2
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
d2jiyl_
L:
2b
d2jiym_
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
d2jiyh1
H:11-35
[
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_2jiyH02 (H:117-249)
2a: CATH_2jiyH01 (H:12-116)
3a: CATH_2jiyM01 (M:2-143)
3b: CATH_2jiyL02 (L:164-263)
3c: CATH_2jiyM02 (M:144-302)
3d: CATH_2jiyL01 (L:1-163)
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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
2jiyH02
H:117-249
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
2jiyH01
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: ncib 8253.
(4)
3a
2jiyM01
M:2-143
3b
2jiyL02
L:164-263
3c
2jiyM02
M:144-302
3d
2jiyL01
L:1-163
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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Chain M
Asymmetric Unit 1
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