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3D38
Asym. Unit
Info
Asym.Unit (223 KB)
Biol.Unit 1 (209 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF NEW TRIGONAL FORM OF PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS. CRYSTALS GROWN IN MICROFLUIDICS BY DETERGENT CAPTURE.
Authors
:
L. Li, S. H. M. Nachtergaele, A. M. Seddon, V. Tereshko, N. Ponomarenko, R. F. Ismagilov, Accelerated Technologies Center For Gene To 3 Structure (Atcg3D)
Date
:
09 May 08 (Deposition) - 08 Jul 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.21
Chains
:
Asym. Unit : C,H,L,M
Biol. Unit 1: C,H,L,M (1x)
Keywords
:
Detergent Extraction, Reaction Center, Microfludics, Plugs, Structural Genomics, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D, Electron Transport, Heme, Iron, Lipoprotein, Membrane, Metal- Binding, Photosynthesis, Transport, Bacteriochlorophyll, Chlorophyll, Chromophore, Formylation, Transmembrane, Magnesium
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Li, S. Nachtergaele, A. M. Seddon, V. Tereshko, N. Ponomarenko, R. F. Ismagilov
Simple Host-Guest Chemistry To Modulate The Process Of Concentration And Crystallization Of Membrane Proteins By Detergent Capture In A Microfluidic Device.
J. Am. Chem. Soc. V. 130 14324 2008
[
close entry info
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Hetero Components
(11, 38)
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: FE (II) ION (FE2a)
04a: N-FORMYLMETHIONINE (FMEa)
05a: HEME C (HECa)
05b: HEME C (HECb)
05c: HEME C (HECc)
05d: HEME C (HECd)
06a: HEPTANE-1,2,3-TRIOL (HTOa)
06b: HEPTANE-1,2,3-TRIOL (HTOb)
06c: HEPTANE-1,2,3-TRIOL (HTOc)
07a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
07b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
07c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
07d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
08a: MENAQUINONE-9 (MQ9a)
09a: 15-CIS-1,2-DIHYDRONEUROSPORENE (NS5a)
10a: SULFATE ION (SO4a)
10b: SULFATE ION (SO4b)
10c: SULFATE ION (SO4c)
10d: SULFATE ION (SO4d)
10e: SULFATE ION (SO4e)
10f: SULFATE ION (SO4f)
10g: SULFATE ION (SO4g)
10h: SULFATE ION (SO4h)
10i: SULFATE ION (SO4i)
10j: SULFATE ION (SO4j)
10k: SULFATE ION (SO4k)
10l: SULFATE ION (SO4l)
10m: SULFATE ION (SO4m)
10n: SULFATE ION (SO4n)
10o: SULFATE ION (SO4o)
11a: UBIQUINONE-1 (UQ1a)
11b: UBIQUINONE-1 (UQ1b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BCB
4
Ligand/Ion
BACTERIOCHLOROPHYLL B
2
BPB
2
Ligand/Ion
BACTERIOPHEOPHYTIN B
3
FE2
1
Ligand/Ion
FE (II) ION
4
FME
1
Mod. Amino Acid
N-FORMYLMETHIONINE
5
HEC
4
Ligand/Ion
HEME C
6
HTO
3
Ligand/Ion
HEPTANE-1,2,3-TRIOL
7
LDA
4
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
8
MQ9
1
Ligand/Ion
MENAQUINONE-9
9
NS5
1
Ligand/Ion
15-CIS-1,2-DIHYDRONEUROSPORENE
10
SO4
15
Ligand/Ion
SULFATE ION
11
UQ1
2
Ligand/Ion
UBIQUINONE-1
[
close Hetero Component info
]
Sites
(37, 37)
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)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS L:190 , HIS L:230 , HIS M:217 , GLU M:232 , HIS M:264
BINDING SITE FOR RESIDUE FE2 M 500
02
AC2
SOFTWARE
ASN L:199 , HIS M:143 , ARG M:265
BINDING SITE FOR RESIDUE SO4 M 801
03
AC3
SOFTWARE
TRP M:23 , TYR M:50 , GLY M:52 , ALA M:53 , SER M:54 , SER M:133
BINDING SITE FOR RESIDUE SO4 M 802
04
AC4
SOFTWARE
THR H:250 , ARG H:253
BINDING SITE FOR RESIDUE SO4 H 803
05
AC5
SOFTWARE
LEU H:246 , ALA M:1 , ARG M:226
BINDING SITE FOR RESIDUE SO4 M 804
06
AC6
SOFTWARE
SER M:35 , TYR M:36 , TRP M:37
BINDING SITE FOR RESIDUE SO4 M 805
07
AC7
SOFTWARE
ARG H:37 , TYR H:41 , GLU H:61 , ARG M:251
BINDING SITE FOR RESIDUE SO4 H 806
08
AC8
SOFTWARE
TYR H:117 , GLU H:119 , ARG H:233 , LYS H:237
BINDING SITE FOR RESIDUE SO4 H 807
09
AC9
SOFTWARE
ALA C:319 , SER C:320 , ARG C:321
BINDING SITE FOR RESIDUE SO4 C 808
10
BC1
SOFTWARE
GLU C:112 , ARG C:115
BINDING SITE FOR RESIDUE SO4 C 809
11
BC2
SOFTWARE
ASN C:196 , LYS C:198 , ARG C:199
BINDING SITE FOR RESIDUE SO4 C 810
12
BC3
SOFTWARE
HIS C:162 , ARG C:165 , ASP L:70 , LYS L:72 , TYR L:73 , GLU L:82
BINDING SITE FOR RESIDUE SO4 C 811
13
BC4
SOFTWARE
HIS H:72 , ASP H:129
BINDING SITE FOR RESIDUE SO4 H 812
14
BC5
SOFTWARE
THR C:161 , HIS C:162 , LYS L:72
BINDING SITE FOR RESIDUE SO4 C 813
15
BC6
SOFTWARE
LYS C:258 , ARG C:293
BINDING SITE FOR RESIDUE SO4 C 814
16
BC7
SOFTWARE
PRO C:160 , ARG C:165 , PRO M:306
BINDING SITE FOR RESIDUE SO4 C 815
17
BC8
SOFTWARE
TYR C:56 , LYS C:57 , ASN C:58 , LYS C:60 , LEU C:62 , PHE C:70 , LEU C:71 , MET C:74 , THR C:75 , ILE C:77 , THR C:78 , CYS C:87 , CYS C:90 , HIS C:91 , LEU C:96 , ALA C:97 , TYR C:104 , ALA C:107 , ARG C:108
BINDING SITE FOR RESIDUE HEC C 401
18
BC9
SOFTWARE
TYR C:89 , TYR C:102 , 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 , ARG C:293 , PRO C:301
BINDING SITE FOR RESIDUE HEC C 402
19
CC1
SOFTWARE
ARG C:202 , PHE C:230 , MET C:233 , MET C:234 , ILE C:236 , SER C:237 , LEU C:240 , 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 , ILE M:189
BINDING SITE FOR RESIDUE HEC C 403
20
CC2
SOFTWARE
HIS C:124 , THR C:128 , ILE C:236 , LEU C:240 , PHE C:246 , GLN C:263 , ILE C:266 , GLY C:270 , ILE C:271 , MET C:273 , CYS C:305 , CYS C:308 , HIS C:309 , THR C:313 , LYS C:314 , PRO C:315
BINDING SITE FOR RESIDUE HEC C 404
21
CC3
SOFTWARE
PHE L:97 , PRO L:124 , MET L:127 , PHE L:128 , ASN L:158 , PHE L:160 , GLY L:161 , TYR L:162 , TRP L:167 , HIS L:168 , HIS L:173 , SER L:176 , ILE L:240 , PHE L:241 , GLY L:244 , THR L:248 , TYR M:195 , TYR M:208
BINDING SITE FOR RESIDUE BCB L 400
22
CC4
SOFTWARE
PHE L:128 , PHE L:146 , ILE L:150 , HIS L:153 , LEU L:154 , GLY M:201 , ILE M:204 , GLY M:205 , TYR M:208 , GLY M:209
BINDING SITE FOR RESIDUE BCB L 401
23
CC5
SOFTWARE
PHE L:41 , ILE L:42 , PHE L:97 , TRP L:100 , GLU L:104 , PHE L:121 , PRO L:124 , TYR L:148 , GLY L:149 , ILE L:150 , HIS L:153 , ALA L:237 , PHE L:241 , TYR M:208 , GLY M:211 , LEU M:212 , TRP M:250
BINDING SITE FOR RESIDUE BPB L 402
24
CC6
SOFTWARE
TYR L:29 , ILE L:39 , PHE L:43 , TRP L:100 , HIS M:217 , ALA M:246 , TRP M:250 , ILE M:254 , ASN M:257 , ALA M:258 , TRP M:266
BINDING SITE FOR RESIDUE MQ9 M 501
25
CC7
SOFTWARE
LEU L:189 , HIS L:190 , LEU L:193 , GLU L:212 , ASN L:213 , PHE L:216 , SER L:223 , ILE L:224 , GLY L:225 , ILE L:229
BINDING SITE FOR RESIDUE UQ1 L 502
26
CC8
SOFTWARE
TRP L:266 , PHE M:85 , PHE M:88 , PHE M:89
BINDING SITE FOR RESIDUE UQ1 L 503
27
CC9
SOFTWARE
HIS L:168 , MET L:174 , SER L:178 , PHE L:181 , MET L:185 , ILE M:177 , TRP M:178 , HIS M:180 , ILE M:181 , LEU M:184
BINDING SITE FOR RESIDUE BCB M 400
28
DC1
SOFTWARE
TYR L:162 , PHE L:181 , GLY M:62 , LEU M:124 , PHE M:154 , LEU M:184 , THR M:185 , PHE M:187 , 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
BINDING SITE FOR RESIDUE BCB M 401
29
DC2
SOFTWARE
PHE L:181 , ALA L:184 , MET L:185 , LEU L:189 , ALA M:58 , PHE M:59 , SER M:123 , LEU M:124 , TRP M:127 , ILE M:144 , ASN M:147 , PHE M:148 , SER M:271
BINDING SITE FOR RESIDUE BPB M 402
30
DC3
SOFTWARE
LEU M:70 , LEU M:114 , GLY M:117 , THR M:121 , GLY M:159 , CYS M:160 , PHE M:175 , GLY M:176 , ILE M:177 , HIS M:180
BINDING SITE FOR RESIDUE NS5 M 600
31
DC4
SOFTWARE
ARG H:33 , ASP H:56
BINDING SITE FOR RESIDUE LDA H 701
32
DC5
SOFTWARE
TRP H:17 , ASP L:60 , TYR M:195 , PRO M:198 , TRP M:295 , HIS M:299
BINDING SITE FOR RESIDUE LDA L 702
33
DC6
SOFTWARE
LEU H:30 , ARG H:34 , TYR H:60 , LEU H:62 , TYR H:64
BINDING SITE FOR RESIDUE LDA H 703
34
DC7
SOFTWARE
ALA M:53 , LEU M:122
BINDING SITE FOR RESIDUE LDA M 704
35
DC8
SOFTWARE
PRO H:71 , HIS H:72 , ASP H:125 , ALA H:126
BINDING SITE FOR RESIDUE HTO H 705
36
DC9
SOFTWARE
PRO C:205 , GLN C:206 , ARG C:221
BINDING SITE FOR RESIDUE HTO C 706
37
EC1
SOFTWARE
GLU C:21 , GLY C:241 , THR C:313
BINDING SITE FOR RESIDUE HTO C 707
[
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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: 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
View:
Label:
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_d3d38c1 (C:1-332)
2a: SCOP_d3d38h1 (H:37-258)
3a: SCOP_d3d38l1 (L:1-273)
4a: SCOP_d3d38m1 (M:1-323)
5a: SCOP_d3d38h2 (H:1-36)
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Classes
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)
(
)
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
d3d38c1
C:1-332
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
d3d38h1
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
:
L (light) subunit
(70)
Rhodopseudomonas viridis [TaxId: 1079]
(10)
3a
d3d38l1
L:1-273
Protein domain
:
M (medium) subunit
(70)
Rhodopseudomonas viridis [TaxId: 1079]
(10)
4a
d3d38m1
M:1-323
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)
5a
d3d38h2
H:1-36
[
close SCOP info
]
CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_3d38H02 (H:120-258)
2a: CATH_3d38H01 (H:2-119)
3a: CATH_3d38C02 (C:143-205,C:221-313)
3b: CATH_3d38C01 (C:24-142,C:314-332)
4a: CATH_3d38M01 (M:1-143)
4b: CATH_3d38M02 (M:144-302)
4c: CATH_3d38L01 (L:1-165)
4d: CATH_3d38L02 (L:166-273)
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Topologies
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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)
Blastochloris viridis. Organism_taxid: 1079.
(10)
1a
3d38H02
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)
Blastochloris viridis. Organism_taxid: 1079.
(10)
2a
3d38H01
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)
Blastochloris viridis. Organism_taxid: 1079.
(10)
3a
3d38C02
C:143-205,C:221-313
3b
3d38C01
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)
Blastochloris viridis. Organism_taxid: 1079.
(10)
4a
3d38M01
M:1-143
4b
3d38M02
M:144-302
4c
3d38L01
L:1-165
4d
3d38L02
L:166-273
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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