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1S00
Asym. Unit
Info
Asym.Unit (299 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (145 KB)
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(1)
Title
:
PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-SEPARATED D+QAQB- STATE
Authors
:
Q. Xu, H. L. Axelrod, E. C. Abresch, M. L. Paddock, M. Y. Okamura, G. Feher
Date
:
29 Dec 03 (Deposition) - 13 Apr 04 (Release) - 25 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : H,L,M,R,S,T
Biol. Unit 1: H,L,M (1x)
Biol. Unit 2: R,S,T (1x)
Keywords
:
Bacterial Photosynthesis, Rhodobacter Sphaeroides, Proton Transfer Pathway, Revertant, Integral Membrane Protein, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Q. Xu, H. L. Axelrod, E. C. Abresch, M. L. Paddock, M. Y. Okamura, G. Fehe
X-Ray Structure Determination Of Three Mutants Of The Bacterial Photosynthetic Reaction Centers From Rb. Sphaeroides; Altered Proton Transfer Pathways.
Structure V. 12 703 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(6, 21)
Info
All Hetero Components
1a: BACTERIOCHLOROPHYLL A (BCLa)
1b: BACTERIOCHLOROPHYLL A (BCLb)
1c: BACTERIOCHLOROPHYLL A (BCLc)
1d: BACTERIOCHLOROPHYLL A (BCLd)
1e: BACTERIOCHLOROPHYLL A (BCLe)
1f: BACTERIOCHLOROPHYLL A (BCLf)
1g: BACTERIOCHLOROPHYLL A (BCLg)
1h: BACTERIOCHLOROPHYLL A (BCLh)
2a: BACTERIOPHEOPHYTIN A (BPHa)
2b: BACTERIOPHEOPHYTIN A (BPHb)
2c: BACTERIOPHEOPHYTIN A (BPHc)
2d: BACTERIOPHEOPHYTIN A (BPHd)
3a: FE (II) ION (FE2a)
3b: FE (II) ION (FE2b)
4a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
5a: SPHEROIDENE (SPOa)
5b: SPHEROIDENE (SPOb)
6a: UBIQUINONE-10 (U10a)
6b: UBIQUINONE-10 (U10b)
6c: UBIQUINONE-10 (U10c)
6d: UBIQUINONE-10 (U10d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCL
8
Ligand/Ion
BACTERIOCHLOROPHYLL A
2
BPH
4
Ligand/Ion
BACTERIOPHEOPHYTIN A
3
FE2
2
Ligand/Ion
FE (II) ION
4
LDA
1
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
5
SPO
2
Ligand/Ion
SPHEROIDENE
6
U10
4
Ligand/Ion
UBIQUINONE-10
[
close Hetero Component info
]
Sites
(21, 21)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:168 , MET L:174 , ILE L:177 , SER L:178 , PHE L:181 , THR L:182 , LEU L:185 , BCL L:1002 , HOH L:1035 , MET M:122 , ILE M:179 , HIS M:182 , LEU M:183 , BCL M:1003 , BPH M:1005 , SPO M:1010
BINDING SITE FOR RESIDUE BCL L 1001
02
AC2
SOFTWARE
PHE L:97 , ALA L:127 , LEU L:131 , VAL L:157 , THR L:160 , GLY L:161 , 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 , ALA L:245 , CYS L:247 , MET L:248 , BCL L:1001 , BCL L:1004 , BPH L:1006 , TYR M:210 , BCL M:1003
BINDING SITE FOR RESIDUE BCL L 1002
03
AC3
SOFTWARE
TYR L:128 , LEU L:131 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , BCL L:1002 , BPH L:1006 , PHE M:197 , GLY M:203 , ILE M:206 , ALA M:207 , TYR M:210 , LEU M:214 , BCL M:1003 , U10 M:1008 , HOH M:1046
BINDING SITE FOR RESIDUE BCL L 1004
04
AC4
SOFTWARE
ILE L:49 , CYS L:92 , ALA L:93 , PHE L:97 , TRP L:100 , GLU L:104 , ILE L:117 , ALA L:120 , PHE L:121 , PHE L:123 , ALA L:124 , TYR L:148 , HIS L:153 , VAL L:241 , BCL L:1002 , BCL L:1004 , TYR M:210 , ALA M:213 , LEU M:214 , TRP M:252 , MET M:256 , U10 M:1008
BINDING SITE FOR RESIDUE BPH L 1006
05
AC5
SOFTWARE
THR L:182 , LEU L:189 , HIS L:190 , LEU L:193 , VAL L:194 , GLU L:212 , PHE L:216 , VAL L:220 , GLY L:221 , TYR L:222 , SER L:223 , ILE L:224 , GLY L:225 , THR L:226 , ILE L:229 , HOH M:1015
BINDING SITE FOR RESIDUE U10 L 1009
06
AC6
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:219 , GLU M:234 , HIS M:266
BINDING SITE FOR RESIDUE FE2 M 1007
07
AC7
SOFTWARE
VAL L:157 , TYR L:162 , PHE L:181 , BCL L:1001 , BCL L:1002 , BCL L:1004 , MET M:122 , 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 , LEU M:209 , TYR M:210 , THR M:277 , GLY M:280 , ILE M:284 , BPH M:1005
BINDING SITE FOR RESIDUE BCL M 1003
08
AC8
SOFTWARE
PHE L:181 , ALA L:184 , LEU L:185 , LEU L:189 , BCL L:1001 , SER M:59 , LEU M:60 , GLY M:63 , ALA M:125 , TRP M:129 , THR M:146 , ALA M:149 , PHE M:150 , ALA M:153 , THR M:277 , BCL M:1003
BINDING SITE FOR RESIDUE BPH M 1005
09
AC9
SOFTWARE
TRP L:100 , BCL L:1004 , BPH L:1006 , MET M:218 , HIS M:219 , THR M:222 , ILE M:223 , ALA M:248 , ALA M:249 , TRP M:252 , MET M:256 , ASN M:259 , ALA M:260 , THR M:261 , MET M:262 , ILE M:265 , TRP M:268 , MET M:272
BINDING SITE FOR RESIDUE U10 M 1008
10
BC1
SOFTWARE
BCL L:1001 , PHE M:67 , ILE M:70 , GLY M:71 , ILE M:72 , TRP M:75 , PHE M:85 , LEU M:89 , SER M:119 , MET M:122 , TRP M:157 , GLY M:161 , PHE M:162 , TRP M:171 , TYR M:177 , GLY M:178 , HIS M:182
BINDING SITE FOR RESIDUE SPO M 1010
11
BC2
SOFTWARE
HIS M:145 , TRP M:148 , ILE M:270
BINDING SITE FOR RESIDUE LDA M 1011
12
BC3
SOFTWARE
PHE R:97 , ALA R:127 , LEU R:131 , VAL R:157 , GLY R:161 , TYR R:162 , ASN R:166 , PHE R:167 , HIS R:168 , HIS R:173 , ILE R:177 , PHE R:180 , SER R:244 , ALA R:245 , CYS R:247 , MET R:248 , BPH R:2006 , TYR S:210 , BCL S:2001 , BCL S:2003 , BCL S:2004
BINDING SITE FOR RESIDUE BCL R 2002
13
BC4
SOFTWARE
THR R:38 , PHE R:41 , ALA R:42 , ILE R:49 , CYS R:92 , ALA R:93 , PHE R:97 , TRP R:100 , GLU R:104 , ILE R:117 , ALA R:120 , PHE R:121 , PHE R:123 , ALA R:124 , PHE R:146 , TYR R:148 , HIS R:153 , VAL R:241 , BCL R:2002 , TYR S:210 , ALA S:213 , LEU S:214 , TRP S:252 , BCL S:2004 , U10 S:2008
BINDING SITE FOR RESIDUE BPH R 2006
14
BC5
SOFTWARE
THR R:182 , LEU R:189 , HIS R:190 , LEU R:193 , GLU R:212 , ASN R:213 , PHE R:216 , TYR R:222 , SER R:223 , ILE R:224 , GLY R:225 , THR R:226 , ILE R:229 , BCL S:2001 , HOH S:2023
BINDING SITE FOR RESIDUE U10 R 2009
15
BC6
SOFTWARE
HIS R:190 , HIS R:230 , HIS S:219 , GLU S:234 , HIS S:266
BINDING SITE FOR RESIDUE FE2 S 2007
16
BC7
SOFTWARE
HIS R:168 , MET R:174 , ILE R:177 , SER R:178 , THR R:182 , BCL R:2002 , U10 R:2009 , HOH R:2014 , MET S:122 , TRP S:157 , ILE S:179 , HIS S:182 , LEU S:183 , BCL S:2003 , BPH S:2005 , SPO S:2010
BINDING SITE FOR RESIDUE BCL S 2001
17
BC8
SOFTWARE
VAL R:157 , TYR R:162 , PHE R:181 , BCL R:2002 , ALA S:153 , LEU S:156 , TRP S:157 , THR S:186 , ASN S:187 , PHE S:189 , SER S:190 , LEU S:196 , PHE S:197 , HIS S:202 , SER S:205 , ILE S:206 , LEU S:209 , TYR S:210 , VAL S:276 , THR S:277 , GLY S:280 , ILE S:284 , BCL S:2001 , BCL S:2004 , BPH S:2005
BINDING SITE FOR RESIDUE BCL S 2003
18
BC9
SOFTWARE
ILE R:46 , LEU R:131 , PHE R:146 , ILE R:150 , HIS R:153 , LEU R:154 , BCL R:2002 , BPH R:2006 , PHE S:197 , GLY S:203 , ILE S:206 , ALA S:207 , TYR S:210 , LEU S:214 , BCL S:2003 , HOH S:2026
BINDING SITE FOR RESIDUE BCL S 2004
19
CC1
SOFTWARE
PHE R:181 , ALA R:184 , LEU R:185 , LEU R:189 , LEU R:219 , VAL R:220 , SER S:59 , LEU S:60 , ALA S:125 , TRP S:129 , THR S:146 , ALA S:149 , PHE S:150 , ALA S:153 , ALA S:273 , VAL S:274 , THR S:277 , BCL S:2001 , BCL S:2003
BINDING SITE FOR RESIDUE BPH S 2005
20
CC2
SOFTWARE
TRP R:100 , BPH R:2006 , MET S:218 , HIS S:219 , THR S:222 , ALA S:248 , ALA S:249 , TRP S:252 , MET S:256 , ASN S:259 , ALA S:260 , THR S:261 , MET S:262 , ILE S:265 , TRP S:268 , MET S:272
BINDING SITE FOR RESIDUE U10 S 2008
21
CC3
SOFTWARE
PHE S:67 , PHE S:68 , ILE S:70 , GLY S:71 , TRP S:75 , PHE S:85 , SER S:119 , MET S:122 , PHE S:123 , TRP S:157 , LEU S:160 , GLY S:161 , PHE S:162 , TRP S:171 , GLY S:178 , ILE S:179 , HIS S:182 , BCL S:2001
BINDING SITE FOR RESIDUE SPO S 2010
[
close Site info
]
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, 4)
Info
All PROSITE Patterns/Profiles
1: REACTION_CENTER (L:166-192,R:166-192,L:166-192,R:16...)
;
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
2
L:166-192
R:166-192
RCEL_RHOSH
167-193
2
L:166-192
R:166-192
RCEM_RHOS4
196-222
2
M:195-221
S:195-221
RCEM_RHOSH
196-222
2
M:195-221
S:195-221
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1s00h1 (H:36-256)
1b: SCOP_d1s00t1 (T:36-256)
2a: SCOP_d1s00l_ (L:)
2b: SCOP_d1s00r_ (R:)
3a: SCOP_d1s00m_ (M:)
3b: SCOP_d1s00s_ (S:)
4a: SCOP_d1s00h2 (H:11-35)
4b: SCOP_d1s00t2 (T:11-35)
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Superfamilies
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)
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
d1s00h1
H:36-256
1b
d1s00t1
T:36-256
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
d1s00l_
L:
2b
d1s00r_
R:
Protein domain
:
M (medium) subunit
(70)
Rhodobacter sphaeroides [TaxId: 1063]
(59)
3a
d1s00m_
M:
3b
d1s00s_
S:
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
d1s00h2
H:11-35
4b
d1s00t2
T:11-35
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1s00H02 (H:117-248)
1b: CATH_1s00T02 (T:117-248)
2a: CATH_1s00H01 (H:12-116)
2b: CATH_1s00T01 (T:12-116)
3a: CATH_1s00S01 (S:3-143)
3b: CATH_1s00M02 (M:144-301)
3c: CATH_1s00S02 (S:144-301)
3d: CATH_1s00L01 (L:1-163)
3e: CATH_1s00R01 (R:1-163)
3f: CATH_1s00L02 (L:164-263)
3g: CATH_1s00R02 (R:164-263)
3h: CATH_1s00M01 (M:1-143)
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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.
(12)
1a
1s00H02
H:117-248
1b
1s00T02
T: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
1s00H01
H:12-116
2b
1s00T01
T: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
1s00S01
S:3-143
3b
1s00M02
M:144-301
3c
1s00S02
S:144-301
3d
1s00L01
L:1-163
3e
1s00R01
R:1-163
3f
1s00L02
L:164-263
3g
1s00R02
R:164-263
3h
1s00M01
M:1-143
[
close CATH info
]
Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_PRC_1s00T01 (T:141-212)
1b: PFAM_PRC_1s00T02 (T:141-212)
2a: PFAM_PRCH_1s00T03 (T:11-137)
2b: PFAM_PRCH_1s00T04 (T:11-137)
3a: PFAM_Photo_RC_1s00R01 (R:29-272)
3b: PFAM_Photo_RC_1s00R02 (R:29-272)
3c: PFAM_Photo_RC_1s00S01 (S:50-301)
3d: PFAM_Photo_RC_1s00S02 (S:50-301)
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Clan
:
PRC-barrel
(43)
Family
:
PRC
(42)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
1a
PRC-1s00T01
T:141-212
1b
PRC-1s00T02
T:141-212
Clan
:
no clan defined [family: PRCH]
(40)
Family
:
PRCH
(40)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
2a
PRCH-1s00T03
T:11-137
2b
PRCH-1s00T04
T:11-137
Clan
:
no clan defined [family: Photo_RC]
(43)
Family
:
Photo_RC
(43)
Rhodobacter sphaeroides (Rhodopseudomonas sphaeroides)
(39)
3a
Photo_RC-1s00R01
R:29-272
3b
Photo_RC-1s00R02
R:29-272
3c
Photo_RC-1s00S01
S:50-301
3d
Photo_RC-1s00S02
S:50-301
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Asym.Unit (299 KB)
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