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3A13
Biol. Unit 2
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Asym.Unit (731 KB)
Biol.Unit 1 (721 KB)
Biol.Unit 2 (720 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF TYPE III RUBISCO SP4 MUTANT COMPLEXED WITH 2-CABP AND ACTIVATED WITH CA
Authors
:
Y. Nishitani, M. Fujihashi, T. Doi, S. Yoshida, H. Atomi, T. Imanaka, K. Miki
Date
:
25 Mar 09 (Deposition) - 07 Apr 10 (Release) - 07 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.34
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (2x)
Biol. Unit 2: F,G,H,I,J (2x)
Keywords
:
Ribulose-1, 2-Bisphosphate Carboxylase/Oxygenase, Rubisco, Lyase, Carbon Dioxide Fixation, Magnesium, Metal-Binding, Monooxygenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Nishitani, M. Fujihashi, T. Doi, S. Yoshida, H. Atomi, T. Imanaka, K. Miki
Sturcture-Based Optimization Of A Type Iii Rubisco From A Hyperthermophile
To Be Published
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Hetero Components
(2, 20)
Info
All Hetero Components
2a: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPa)
2b: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPb)
2c: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPc)
2d: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPd)
2e: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPe)
2f: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPf)
2g: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPg)
2h: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPh)
2i: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPi)
2j: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPj)
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
3f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
3h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
3i: LYSINE NZ-CARBOXYLIC ACID (KCXi)
3j: LYSINE NZ-CARBOXYLIC ACID (KCXj)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CAP
10
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
3
KCX
10
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
MG
-1
Ligand/Ion
MAGNESIUM ION
[
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]
Sites
(10, 10)
Info
All Sites
01: BC2 (SOFTWARE)
02: BC3 (SOFTWARE)
03: BC4 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
BC2
SOFTWARE
KCX F:189 , ASP F:191 , GLU F:192 , CAP F:446
BINDING SITE FOR RESIDUE MG F 445
02
BC3
SOFTWARE
LYS F:163 , LYS F:165 , KCX F:189 , ASP F:191 , GLU F:192 , HIS F:281 , ARG F:282 , HIS F:314 , LYS F:322 , LEU F:323 , SER F:367 , GLY F:368 , GLY F:369 , GLN F:389 , GLY F:391 , GLY F:392 , MG F:445 , HOH F:520 , HOH F:524 , HOH F:528 , HOH F:541 , HOH F:562 , HOH F:570 , HOH F:623 , GLU H:49 , THR H:54 , TRP H:55 , ASN H:111
BINDING SITE FOR RESIDUE CAP F 446
03
BC4
SOFTWARE
LYS G:163 , LYS G:165 , KCX G:189 , ASP G:191 , GLU G:192 , CAP G:446
BINDING SITE FOR RESIDUE MG G 445
04
BC5
SOFTWARE
GLU G:49 , TRP G:55 , ASN G:111 , LYS G:163 , LYS G:165 , KCX G:189 , ASP G:191 , GLU G:192 , HIS G:281 , ARG G:282 , HIS G:314 , LYS G:322 , LEU G:323 , SER G:367 , GLY G:368 , GLY G:369 , GLN G:389 , GLY G:391 , GLY G:392 , MG G:445 , HOH G:503 , HOH G:528 , HOH G:536 , HOH G:582 , HOH G:603 , HOH G:669 , HOH G:672
BINDING SITE FOR RESIDUE CAP G 446
05
BC6
SOFTWARE
LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , CAP H:446
BINDING SITE FOR RESIDUE MG H 445
06
BC7
SOFTWARE
TRP F:55 , ASN F:111 , HOH F:519 , LYS H:163 , LYS H:165 , KCX H:189 , GLU H:192 , HIS H:281 , ARG H:282 , HIS H:314 , LYS H:322 , LEU H:323 , SER H:367 , GLY H:368 , GLY H:369 , GLN H:389 , GLY H:391 , GLY H:392 , MG H:445 , HOH H:535 , HOH H:543 , HOH H:607 , HOH H:652
BINDING SITE FOR RESIDUE CAP H 446
07
BC8
SOFTWARE
LYS I:163 , KCX I:189 , ASP I:191 , GLU I:192 , CAP I:446
BINDING SITE FOR RESIDUE MG I 445
08
BC9
SOFTWARE
LYS I:163 , LYS I:165 , KCX I:189 , ASP I:191 , GLU I:192 , HIS I:281 , ARG I:282 , HIS I:314 , LYS I:322 , LEU I:323 , SER I:367 , GLY I:368 , GLY I:369 , GLN I:389 , GLY I:391 , GLY I:392 , MG I:445 , HOH I:536 , HOH I:537 , HOH I:543 , HOH I:547 , HOH I:575 , HOH I:659 , HOH I:673 , GLU J:49 , THR J:54 , TRP J:55 , ASN J:111
BINDING SITE FOR RESIDUE CAP I 446
09
CC1
SOFTWARE
KCX J:189 , ASP J:191 , GLU J:192 , CAP J:446 , HOH J:678
BINDING SITE FOR RESIDUE CA J 445
10
CC2
SOFTWARE
TRP I:55 , ASN I:111 , KCX J:189 , GLU J:192 , HIS J:281 , ARG J:282 , HIS J:314 , SER J:367 , GLY J:368 , GLY J:369 , GLN J:389 , LEU J:390 , GLY J:391 , GLY J:392 , CA J:445 , HOH J:526 , HOH J:538 , HOH J:547 , HOH J:549 , HOH J:586 , HOH J:604 , HOH J:678
BINDING SITE FOR RESIDUE CAP J 446
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 20)
Info
All SCOP Domains
1a: SCOP_d3a13a1 (A:9-135)
1b: SCOP_d3a13b1 (B:8-135)
1c: SCOP_d3a13c1 (C:7-135)
1d: SCOP_d3a13d1 (D:5-135)
1e: SCOP_d3a13e1 (E:8-135)
1f: SCOP_d3a13f1 (F:8-135)
1g: SCOP_d3a13g1 (G:8-135)
1h: SCOP_d3a13h1 (H:7-135)
1i: SCOP_d3a13i1 (I:5-135)
1j: SCOP_d3a13j1 (J:8-135)
2a: SCOP_d3a13a2 (A:136-444)
2b: SCOP_d3a13b2 (B:136-444)
2c: SCOP_d3a13c2 (C:136-444)
2d: SCOP_d3a13d2 (D:136-444)
2e: SCOP_d3a13e2 (E:136-444)
2f: SCOP_d3a13f2 (F:136-444)
2g: SCOP_d3a13g2 (G:136-444)
2h: SCOP_d3a13h2 (H:136-444)
2i: SCOP_d3a13i2 (I:136-444)
2j: SCOP_d3a13j2 (J:136-444)
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)
(
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RuBisCO, large subunit, small (N-terminal) domain
(66)
Family
:
automated matches
(27)
Protein domain
:
automated matches
(27)
Pyrococcus kodakaraensis [TaxId: 69014]
(1)
1a
d3a13a1
A:9-135
1b
d3a13b1
B:8-135
1c
d3a13c1
C:7-135
1d
d3a13d1
D:5-135
1e
d3a13e1
E:8-135
1f
d3a13f1
F:8-135
1g
d3a13g1
G:8-135
1h
d3a13h1
H:7-135
1i
d3a13i1
I:5-135
1j
d3a13j1
J:8-135
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
RuBisCo, C-terminal domain
(66)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Pyrococcus kodakaraensis [TaxId: 69014]
(1)
2a
d3a13a2
A:136-444
2b
d3a13b2
B:136-444
2c
d3a13c2
C:136-444
2d
d3a13d2
D:136-444
2e
d3a13e2
E:136-444
2f
d3a13f2
F:136-444
2g
d3a13g2
G:136-444
2h
d3a13h2
H:136-444
2i
d3a13i2
I:136-444
2j
d3a13j2
J:136-444
[
close SCOP info
]
CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_3a13A01 (A:9-136)
1b: CATH_3a13B01 (B:8-136)
1c: CATH_3a13D01 (D:5-136)
1d: CATH_3a13E01 (E:8-136)
1e: CATH_3a13F01 (F:8-136)
1f: CATH_3a13G01 (G:8-136)
1g: CATH_3a13I01 (I:5-136)
1h: CATH_3a13J01 (J:8-136)
1i: CATH_3a13C01 (C:7-136)
1j: CATH_3a13H01 (H:7-136)
2a: CATH_3a13A02 (A:137-438)
2b: CATH_3a13B02 (B:137-438)
2c: CATH_3a13D02 (D:137-438)
2d: CATH_3a13F02 (F:137-438)
2e: CATH_3a13G02 (G:137-438)
2f: CATH_3a13H02 (H:137-438)
2g: CATH_3a13I02 (I:137-438)
2h: CATH_3a13C02 (C:137-438)
2i: CATH_3a13J02 (J:137-438)
2j: CATH_3a13E02 (E:137-438)
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.150, no name defined]
(49)
Thermococcus kodakaraensis (Pyrococcus kodakaraensis)
(2)
1a
3a13A01
A:9-136
1b
3a13B01
B:8-136
1c
3a13D01
D:5-136
1d
3a13E01
E:8-136
1e
3a13F01
F:8-136
1f
3a13G01
G:8-136
1g
3a13I01
I:5-136
1h
3a13J01
J:8-136
1i
3a13C01
C:7-136
1j
3a13H01
H:7-136
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Thermococcus kodakaraensis (Pyrococcus kodakaraensis)
(2)
2a
3a13A02
A:137-438
2b
3a13B02
B:137-438
2c
3a13D02
D:137-438
2d
3a13F02
F:137-438
2e
3a13G02
G:137-438
2f
3a13H02
H:137-438
2g
3a13I02
I:137-438
2h
3a13C02
C:137-438
2i
3a13J02
J:137-438
2j
3a13E02
E:137-438
[
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Pfam Domains
(0, 0)
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