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3A13
Asym. Unit
Info
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
(4, 30)
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
2
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
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:189 , ASP A:191 , GLU A:192 , CAP A:446
BINDING SITE FOR RESIDUE MG A 445
02
AC2
SOFTWARE
LYS A:163 , LYS A:165 , KCX A:189 , ASP A:191 , GLU A:192 , HIS A:281 , ARG A:282 , HIS A:314 , LYS A:322 , LEU A:323 , SER A:367 , GLY A:368 , GLY A:369 , GLN A:389 , GLY A:391 , GLY A:392 , MG A:445 , HOH A:508 , HOH A:523 , HOH A:528 , HOH A:529 , HOH A:535 , HOH A:554 , HOH A:584 , HOH A:625 , GLU C:49 , THR C:54 , TRP C:55 , ASN C:111
BINDING SITE FOR RESIDUE CAP A 446
03
AC3
SOFTWARE
ASN B:111 , LYS B:163 , LYS B:165 , KCX B:189 , ASP B:191 , GLU B:192 , CAP B:446
BINDING SITE FOR RESIDUE MG B 445
04
AC4
SOFTWARE
GLU B:49 , TRP B:55 , ASN B:111 , LYS B:163 , LYS B:165 , KCX B:189 , ASP B:191 , GLU B:192 , HIS B:281 , ARG B:282 , HIS B:314 , LYS B:322 , LEU B:323 , SER B:367 , GLY B:368 , GLY B:369 , GLN B:389 , GLY B:391 , GLY B:392 , MG B:445 , HOH B:510 , HOH B:516 , HOH B:520 , HOH B:534 , HOH B:554 , HOH B:555 , HOH B:667
BINDING SITE FOR RESIDUE CAP B 446
05
AC5
SOFTWARE
LYS C:163 , KCX C:189 , ASP C:191 , GLU C:192 , CAP C:446
BINDING SITE FOR RESIDUE MG C 445
06
AC6
SOFTWARE
GLU A:49 , TRP A:55 , ASN A:111 , LYS C:163 , LYS C:165 , KCX C:189 , GLU C:192 , HIS C:281 , ARG C:282 , HIS C:314 , LYS C:322 , LEU C:323 , SER C:367 , GLY C:368 , GLY C:369 , GLN C:389 , GLY C:391 , GLY C:392 , MG C:445 , HOH C:518 , HOH C:522 , HOH C:536 , HOH C:553 , HOH C:586 , HOH C:661
BINDING SITE FOR RESIDUE CAP C 446
07
AC7
SOFTWARE
KCX D:189 , ASP D:191 , GLU D:192 , CAP D:446
BINDING SITE FOR RESIDUE MG D 445
08
AC8
SOFTWARE
LYS D:163 , LYS D:165 , KCX D:189 , ASP D:191 , GLU D:192 , HIS D:281 , ARG D:282 , HIS D:314 , LYS D:322 , SER D:367 , GLY D:368 , GLY D:369 , GLN D:389 , GLY D:391 , GLY D:392 , MG D:445 , HOH D:504 , HOH D:521 , HOH D:532 , HOH D:536 , HOH D:601 , HOH D:710 , GLU E:49 , THR E:54 , TRP E:55 , ASN E:111
BINDING SITE FOR RESIDUE CAP D 446
09
AC9
SOFTWARE
KCX E:189 , ASP E:191 , GLU E:192 , CAP E:446 , HOH E:666
BINDING SITE FOR RESIDUE CA E 445
10
BC1
SOFTWARE
TRP D:55 , ASN D:111 , KCX E:189 , GLU E:192 , HIS E:281 , ARG E:282 , HIS E:314 , SER E:367 , GLY E:368 , GLY E:369 , GLN E:389 , LEU E:390 , GLY E:391 , GLY E:392 , CA E:445 , HOH E:528 , HOH E:535 , HOH E:556 , HOH E:577 , HOH E:627 , HOH E:666 , HOH E:687
BINDING SITE FOR RESIDUE CAP E 446
11
BC2
SOFTWARE
KCX F:189 , ASP F:191 , GLU F:192 , CAP F:446
BINDING SITE FOR RESIDUE MG F 445
12
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
13
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
14
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
15
BC6
SOFTWARE
LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , CAP H:446
BINDING SITE FOR RESIDUE MG H 445
16
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
17
BC8
SOFTWARE
LYS I:163 , KCX I:189 , ASP I:191 , GLU I:192 , CAP I:446
BINDING SITE FOR RESIDUE MG I 445
18
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
19
CC1
SOFTWARE
KCX J:189 , ASP J:191 , GLU J:192 , CAP J:446 , HOH J:678
BINDING SITE FOR RESIDUE CA J 445
20
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)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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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
(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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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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Homologous Superfamilies
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)
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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