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2WJM
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (214 KB)
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(1)
Title
:
LIPIDIC SPONGE PHASE CRYSTAL STRUCTURE OF THE PHOTOSYNTHETIC REACTION CENTRE FROM BLASTOCHLORIS VIRIDIS (LOW DOSE)
Authors
:
A. B. Woehri, W. Y. Wahlgren, E. Malmerberg, L. C. Johansson, R. Neutze,
Date
:
27 May 09 (Deposition) - 22 Sep 09 (Release) - 14 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Reaction Centre, Photosynthesis, Membrane Protein, Lipids, Monoolein, Posttranslational Modification, Thioether Bond, Ubiquinone, Lipidic Sponge Phase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. B. Woehri, W. Y. Wahlgren, E. Malmerberg, R. Neutze, G. Katona
Lipidic-Sponge Phase Crystal Structure Of A Photosynthetic Reaction Center Reveals Lipids On The Protein Surface.
Biochemistry V. 48 9831 2009
[
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Hetero Components
(10, 20)
Info
All Hetero Components
01a: BACTERIOCHLOROPHYLL B (BCBa)
01b: BACTERIOCHLOROPHYLL B (BCBb)
01c: BACTERIOCHLOROPHYLL B (BCBc)
01d: BACTERIOCHLOROPHYLL B (BCBd)
02a: BACTERIOPHEOPHYTIN B (BPBa)
02b: BACTERIOPHEOPHYTIN B (BPBb)
03a: DIACYL GLYCEROL (DGAa)
04a: FE (II) ION (FE2a)
05a: N-FORMYLMETHIONINE (FMEa)
06a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
06b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
06c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
06d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
07a: [(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(... (MPGa)
07b: [(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(... (MPGb)
07c: [(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(... (MPGc)
08a: MENAQUINONE-7 (MQ7a)
09a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
10a: PHOSPHATE ION (PO4a)
10b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCB
4
Ligand/Ion
BACTERIOCHLOROPHYLL B
2
BPB
2
Ligand/Ion
BACTERIOPHEOPHYTIN B
3
DGA
1
Ligand/Ion
DIACYL GLYCEROL
4
FE2
1
Ligand/Ion
FE (II) ION
5
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
6
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
7
MPG
3
Ligand/Ion
[(Z)-OCTADEC-9-ENYL] (2R)-2,3-BIS(OXIDANYL)PROPANOATE
8
MQ7
1
Ligand/Ion
MENAQUINONE-7
9
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
10
PO4
2
Ligand/Ion
PHOSPHATE ION
[
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]
Sites
(19, 19)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR C:56 , LYS C:57 , ASN C:58 , VAL C:59 , LYS C:60 , VAL C:61 , LEU C:62 , PHE C:70 , MET C:74 , ILE C:77 , THR C:78 , SER C:82 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , TYR C:104 , ALA C:107 , ARG C:108 , HOH C:501 , HOH C:634 , PRO M:313
binding site for residue HEM C 401
02
AC2
SOFTWARE
ILE C:77 , TYR C:89 , TYR C:102 , PRO C:103 , VAL C:106 , MET C:110 , LEU C:111 , MET C:113 , THR C:114 , THR C:131 , CYS C:132 , CYS C:135 , HIS C:136 , PRO C:140 , LEU C:141 , PRO C:142 , LEU C:289 , ARG C:293 , PRO C:301
binding site for residue HEM C 402
03
AC3
SOFTWARE
ARG C:202 , VAL C:203 , VAL C:204 , MET C:233 , SER C:237 , ASN C:243 , CYS C:244 , CYS C:247 , HIS C:248 , PHE C:253 , GLU C:254 , ARG C:264 , ALA C:267 , TRP C:268 , ARG C:272 , HOH C:521 , HOH C:566 , HOH C:581 , HOH C:593 , ILE M:189
binding site for residue HEM C 403
04
AC4
SOFTWARE
HIS C:124 , VAL C:125 , THR C:128 , GLY C:129 , VAL C:130 , LEU C:240 , PHE C:246 , GLN C:263 , ILE C:266 , ILE C:271 , MET C:273 , ASP C:304 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315 , HOH C:508 , HOH C:534 , HOH C:573 , HOH C:635
binding site for residue HEM C 404
05
AC5
SOFTWARE
CYS C:1 , SER L:178 , TRP L:262 , TRP L:265 , BCB M:401 , NS5 M:405
binding site for residue DGA C 405
06
AC6
SOFTWARE
MET L:127 , PHE L:128 , VAL L:157 , ASN L:158 , PHE L:160 , TYR L:162 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , VAL L:177 , PHE L:181 , ILE L:240 , PHE L:241 , GLY L:244 , THR L:248 , BCB L:302 , BPB L:303 , TYR M:195 , TYR M:208 , BCB M:401 , BCB M:402
binding site for residue BCB L 301
07
AC7
SOFTWARE
VAL L:46 , ILE L:49 , PHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , VAL L:157 , BCB L:301 , BPB L:303 , TYR M:195 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209 , BCB M:402 , HOH M:565
binding site for residue BCB L 302
08
AC8
SOFTWARE
ILE L:42 , PHE L:97 , TRP L:100 , GLU L:104 , VAL L:117 , ALA L:120 , PHE L:121 , PRO L:124 , TYR L:148 , ALA L:237 , PHE L:241 , BCB L:301 , BCB L:302 , TYR M:208 , LEU M:212 , TRP M:250 , ILE M:254 , MQ7 M:404
binding site for residue BPB L 303
09
AC9
SOFTWARE
TRP L:115 , HIS L:116 , LEU L:119 , ARG L:231 , SER L:238 , HOH M:615
binding site for residue MPG L 304
10
AD1
SOFTWARE
HIS L:190 , LEU L:193 , SER L:223 , GLY L:225 , HOH L:461 , MPG M:406
binding site for residue MPG L 305
11
AD2
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264
binding site for residue FE2 L 306
12
AD3
SOFTWARE
DGA C:405 , HIS L:168 , MET L:174 , VAL L:177 , SER L:178 , PHE L:181 , VAL L:182 , BCB L:301 , HOH L:428 , MET M:120 , VAL M:155 , ILE M:158 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , LEU M:184 , BCB M:402 , BPB M:403 , NS5 M:405
binding site for residue BCB M 401
13
AD4
SOFTWARE
TYR L:162 , PHE L:181 , BCB L:301 , BCB L:302 , ILE M:69 , LEU M:124 , PHE M:148 , PHE M:154 , VAL M:155 , SER M:188 , PHE M:194 , TYR M:195 , HIS M:200 , SER M:203 , ILE M:204 , TYR M:208 , MET M:275 , ALA M:278 , ILE M:282 , BCB M:401 , BPB M:403
binding site for residue BCB M 402
14
AD5
SOFTWARE
PHE L:181 , MET L:185 , LEU L:189 , VAL L:220 , PHE M:59 , SER M:63 , ILE M:66 , SER M:123 , LEU M:124 , TRP M:127 , VAL M:131 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271 , MET M:275 , BCB M:401 , BCB M:402 , NS5 M:405
binding site for residue BPB M 403
15
AD6
SOFTWARE
TYR L:29 , ARG L:103 , BPB L:303 , HIS M:217 , THR M:220 , ALA M:246 , ALA M:247 , TRP M:250 , PHE M:256 , ASN M:257 , ALA M:258
binding site for residue MQ7 M 404
16
AD7
SOFTWARE
DGA C:405 , MET M:73 , GLY M:117 , THR M:121 , GLY M:159 , CYS M:160 , TRP M:169 , PHE M:175 , GLY M:176 , ILE M:177 , BCB M:401 , BPB M:403
binding site for residue NS5 M 405
17
AD8
SOFTWARE
VAL L:220 , GLY L:221 , MPG L:305 , LYS M:31
binding site for residue MPG M 406
18
AD9
SOFTWARE
TRP M:23 , TYR M:50 , GLY M:52 , ALA M:53 , SER M:54 , HOH M:509 , HOH M:525
binding site for residue PO4 M 407
19
AE1
SOFTWARE
ASN L:199 , HIS M:143 , ARG M:265 , HOH M:501 , HOH M:505
binding site for residue PO4 M 408
[
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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, 3)
Info
All PROSITE Patterns/Profiles
1: MULTIHEME_CYTC (C:82-314)
2: REACTION_CENTER (L:166-192,M:193-219)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MULTIHEME_CYTC
PS51008
Multiheme cytochrome c family profile.
CYCR_BLAVI
102-334
1
C:82-314
2
REACTION_CENTER
PS00244
Photosynthetic reaction center proteins signature.
RCEL_BLAVI
167-193
1
L:166-192
RCEM_BLAVI
194-220
1
M:193-219
[
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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, 5)
Info
All SCOP Domains
1a: SCOP_d2wjmc_ (C:)
2a: SCOP_d2wjmh2 (H:37-258)
3a: SCOP_d2wjml_ (L:)
3b: SCOP_d2wjmm_ (M:)
4a: SCOP_d2wjmh1 (H:1-36)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Multiheme cytochromes
(149)
Superfamily
:
Multiheme cytochromes
(149)
Family
:
Photosynthetic reaction centre (cytochrome subunit)
(20)
Protein domain
:
Photosynthetic reaction centre (cytochrome subunit)
(19)
Rhodopseudomonas viridis [TaxId: 1079]
(18)
1a
d2wjmc_
C:
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)
Rhodopseudomonas viridis [TaxId: 1079]
(15)
2a
d2wjmh2
H:37-258
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)
Rhodopseudomonas viridis [TaxId: 1079]
(2)
3a
d2wjml_
L:
3b
d2wjmm_
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)
Rhodopseudomonas viridis [TaxId: 1079]
(15)
4a
d2wjmh1
H:1-36
[
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]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_2wjmH02 (H:120-258)
2a: CATH_2wjmH01 (H:2-119)
3a: CATH_2wjmC02 (C:143-205,C:221-313)
3b: CATH_2wjmC01 (C:24-142,C:314-332)
4a: CATH_2wjmM01 (M:1-143)
4b: CATH_2wjmL02 (L:166-273)
4c: CATH_2wjmM02 (M:144-302)
4d: CATH_2wjmL01 (L:1-165)
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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)
Rhodopseudomonas viridis. Organism_taxid: 1079.
(3)
1a
2wjmH02
H:120-258
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)
Rhodopseudomonas viridis. Organism_taxid: 1079.
(3)
2a
2wjmH01
H:2-119
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Photosynthetic Reaction Center, subunit C; domain 2
(18)
Homologous Superfamily
:
Photosynthetic Reaction Center, subunit C, domain 2
(18)
Rhodopseudomonas viridis. Organism_taxid: 1079.
(3)
3a
2wjmC02
C:143-205,C:221-313
3b
2wjmC01
C:24-142,C:314-332
Architecture
:
Up-down Bundle
(3216)
Topology
:
Photosynthetic Reaction Center, subunit M; domain 1
(93)
Homologous Superfamily
:
Membrane spanning alpha-helix pairs
(93)
Rhodopseudomonas viridis. Organism_taxid: 1079.
(3)
4a
2wjmM01
M:1-143
4b
2wjmL02
L:166-273
4c
2wjmM02
M:144-302
4d
2wjmL01
L:1-165
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (228 KB)
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