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1L9B
Asym. Unit
Info
Asym.Unit (177 KB)
Biol.Unit 1 (166 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE CYTOCHROME-C(2)-PHOTOSYNTHETIC REACTION CENTER ELECTRON TRANSFER COMPLEX FROM RHODOBACTER SPHAEROIDES IN TYPE II CO-CRYSTALS
Authors
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Feher
Date
:
22 Mar 02 (Deposition) - 12 Jun 02 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Bacterial Photosynthesis, Protein-Protein Interaction, Electron Transfer Proteins, Membrane Proteins, Protein Complexes, Photosynthesis
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Axelrod, E. C. Abresch, M. Y. Okamura, A. P. Yeh, D. C. Rees, G. Fehe
X-Ray Structure Determination Of The Cytochrome C2: Reactio Center Electron Transfer Complex From Rhodobacter Sphaeroides.
J. Mol. Biol. V. 319 501 2002
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Hetero Components
(9, 22)
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: CHLORIDE ION (CLa)
4a: FE (II) ION (FE2a)
5a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
6a: HEPTANE-1,2,3-TRIOL (HTOa)
6b: HEPTANE-1,2,3-TRIOL (HTOb)
7a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
7b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
7c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
7d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
7e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
7f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
7g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
7h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
7i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
8a: SODIUM ION (NAa)
9a: 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
CL
1
Ligand/Ion
CHLORIDE ION
4
FE2
1
Ligand/Ion
FE (II) ION
5
HEM
1
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
6
HTO
2
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
LDA
9
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
NA
1
Ligand/Ion
SODIUM ION
9
U10
1
Ligand/Ion
UBIQUINONE-10
[
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Sites
(22, 22)
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)
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 1007
02
AC2
SOFTWARE
HIS M:145
BINDING SITE FOR RESIDUE CL M 1010
03
AC3
SOFTWARE
TRP L:266 , PHE M:90
BINDING SITE FOR RESIDUE NA L 1011
04
AC4
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , THR L:182 , BPH L:1005 , ILE M:179 , HIS M:182 , LEU M:183 , THR M:186 , BCL M:1003 , LDA M:1015 , HOH M:1082 , HOH M:1084
BINDING SITE FOR RESIDUE BCL M 1001
05
AC5
SOFTWARE
PHE L:97 , ALA L:124 , LEU L:131 , VAL L:157 , TYR L:162 , ASN L:166 , HIS L:168 , HIS L:173 , ALA L:176 , ILE L:177 , PHE L:180 , SER L:244 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:1004 , HOH L:1109 , BCL M:1003 , BPH M:1006
BINDING SITE FOR RESIDUE BCL L 1002
06
AC6
SOFTWARE
TYR L:162 , PHE L:181 , BCL L:1002 , BPH L:1005 , ALA M:153 , LEU M:156 , TRP M:157 , 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 , THR M:277 , GLY M:280 , GLY M:281 , ILE M:284 , BCL M:1001
BINDING SITE FOR RESIDUE BCL M 1003
07
AC7
SOFTWARE
ILE L:46 , TYR L:128 , LEU L:131 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:1002 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BPH M:1006 , LDA M:1013
BINDING SITE FOR RESIDUE BCL L 1004
08
AC8
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , LEU L:219 , LEU M:60 , GLY M:63 , LEU M:64 , ALA M:125 , VAL M:126 , TRP M:129 , ALA M:149 , PHE M:150 , ALA M:273 , VAL M:274 , THR M:277 , BCL M:1001 , BCL M:1003 , HOH M:1084
BINDING SITE FOR RESIDUE BPH L 1005
09
AC9
SOFTWARE
PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , PHE L:121 , HIS L:153 , SER L:237 , LEU L:238 , VAL L:241 , BCL L:1002 , BCL L:1004 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256
BINDING SITE FOR RESIDUE BPH M 1006
10
BC1
SOFTWARE
HIS M:219 , THR M:222 , TRP M:252 , PHE M:258 , ASN M:259 , ALA M:260 , THR M:261 , MET M:262 , ILE M:265 , MET M:272
BINDING SITE FOR RESIDUE U10 M 1008
11
BC2
SOFTWARE
CYS C:15 , CYS C:18 , HIS C:19 , THR C:36 , PRO C:38 , ARG C:46 , ALA C:48 , GLY C:49 , PHE C:54 , TYR C:57 , GLY C:58 , MET C:61 , TRP C:71 , PHE C:76 , TYR C:79 , LYS C:99 , MET C:100 , THR C:101 , PHE C:102 , HOH C:1041 , HOH C:1057
BINDING SITE FOR RESIDUE HEM C 1009
12
BC3
SOFTWARE
TYR H:30 , ARG M:267 , TRP M:271 , LEU M:278 , HOH M:1072
BINDING SITE FOR RESIDUE LDA M 1012
13
BC4
SOFTWARE
ILE H:28 , BCL L:1004 , LEU M:204 , HOH M:1050
BINDING SITE FOR RESIDUE LDA M 1013
14
BC5
SOFTWARE
MET H:175 , ALA H:176 , MET H:193 , GLN H:194 , HTO L:1021
BINDING SITE FOR RESIDUE LDA H 1014
15
BC6
SOFTWARE
PHE M:67 , PHE M:74 , MET M:122 , TRP M:157 , VAL M:175 , PRO M:176 , TYR M:177 , HIS M:182 , BCL M:1001 , HOH M:1032
BINDING SITE FOR RESIDUE LDA M 1015
16
BC7
SOFTWARE
TRP L:59 , ILE L:64
BINDING SITE FOR RESIDUE LDA L 1016
17
BC8
SOFTWARE
ILE L:49 , PRO L:61
BINDING SITE FOR RESIDUE LDA L 1017
18
BC9
SOFTWARE
VAL L:98 , PRO L:118
BINDING SITE FOR RESIDUE LDA L 1018
19
CC1
SOFTWARE
TRP H:21
BINDING SITE FOR RESIDUE LDA H 1019
20
CC2
SOFTWARE
TRP L:262 , TRP L:265
BINDING SITE FOR RESIDUE LDA L 1020
21
CC3
SOFTWARE
LDA H:1014 , HIS L:116 , ARG L:231
BINDING SITE FOR RESIDUE HTO L 1021
22
CC4
SOFTWARE
GLN C:16 , THR C:17 , ARG C:32 , ALA C:34 , ASP L:155 , ASN L:159 , HOH L:1028 , ASN M:195
BINDING SITE FOR RESIDUE HTO C 1022
[
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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
(2, 3)
Info
All PROSITE Patterns/Profiles
1: CYTC (C:3-121,C:3-121)
2: 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
CYTC
PS51007
Cytochrome c family profile.
CYC2_RHOSH
3-121
1
C:3-121
CYC2_RHOS4
24-142
1
C:3-121
2
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
View:
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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
(5, 5)
Info
All SCOP Domains
1a: SCOP_d1l9bc_ (C:)
2a: SCOP_d1l9bh1 (H:36-253)
3a: SCOP_d1l9bl_ (L:)
4a: SCOP_d1l9bm_ (M:)
5a: SCOP_d1l9bh2 (H:8-35)
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(
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Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cytochrome c
(308)
Superfamily
:
Cytochrome c
(308)
Family
:
monodomain cytochrome c
(197)
Protein domain
:
Cytochrome c2
(21)
Rhodobacter sphaeroides [TaxId: 1063]
(5)
1a
d1l9bc_
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)
Rhodobacter sphaeroides [TaxId: 1063]
(82)
2a
d1l9bh1
H:36-253
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)
3a
d1l9bl_
L:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
4a
d1l9bm_
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)
5a
d1l9bh2
H:8-35
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CATH Domains
(4, 7)
Info
all CATH domains
1a: CATH_1l9bH02 (H:117-249)
2a: CATH_1l9bH01 (H:12-116)
3a: CATH_1l9bC00 (C:1-124)
4a: CATH_1l9bM02 (M:144-301)
4b: CATH_1l9bL01 (L:1-163)
4c: CATH_1l9bL02 (L:164-263)
4d: CATH_1l9bM01 (M:35-143)
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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: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
1a
1l9bH02
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: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
2a
1l9bH01
H:12-116
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome Bc1 Complex; Chain D, domain 2
(279)
Homologous Superfamily
:
Cytochrome c
(279)
Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
3a
1l9bC00
C:1-124
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: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26. Rhodobacter sphaeroides. Organism_taxid: 1063. Strain: r26.
(2)
4a
1l9bM02
M:144-301
4b
1l9bL01
L:1-163
4c
1l9bL02
L:164-263
4d
1l9bM01
M:35-143
[
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Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_PRC_1l9bH01 (H:141-212)
2a: PFAM_PRCH_1l9bH02 (H:8-137)
3a: PFAM_Photo_RC_1l9bL01 (L:29-272)
3b: PFAM_Photo_RC_1l9bM01 (M:50-301)
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Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1l9bH01
H:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1l9bH02
H:8-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1l9bL01
L:29-272
3b
Photo_RC-1l9bM01
M:50-301
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