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3JR2
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (78 KB)
Biol.Unit 2 (76 KB)
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(1)
Title
:
X-RAY CRYSTAL STRUCTURE OF THE MG-BOUND 3-KETO-L-GULONATE-6-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR EL TOR STR. N16961
Authors
:
B. Nocek, N. Maltseva, J. Stam, W. Anderson, A. Joachimiak, Csgid
Date
:
08 Sep 09 (Deposition) - 13 Oct 09 (Release) - 08 Feb 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
3-Keto-L-Gulonate-6-Phosphate Decarboxylase, Ulad, Csgid, Mg-Bound, Biosynthetic Protein, Structural Genomics, Center For Structural Genomics Of Infectious Diseases
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Nocek, N. Maltseva, J. Stam, W. Anderson, A. Joachimiak, Csgid
Crystal Structure Of The Mg-Bound 3-Keto-L-Gulonate-6-Phosphate Decarboxylase From Vibrio Cholerae O1 Biovar El Tor Str. N16961
To Be Published
[
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Hetero Components
(5, 49)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
4a: SELENOMETHIONINE (MSEa)
4b: SELENOMETHIONINE (MSEb)
4c: SELENOMETHIONINE (MSEc)
4d: SELENOMETHIONINE (MSEd)
4e: SELENOMETHIONINE (MSEe)
4f: SELENOMETHIONINE (MSEf)
4g: SELENOMETHIONINE (MSEg)
4h: SELENOMETHIONINE (MSEh)
4i: SELENOMETHIONINE (MSEi)
4j: SELENOMETHIONINE (MSEj)
4k: SELENOMETHIONINE (MSEk)
4l: SELENOMETHIONINE (MSEl)
4m: SELENOMETHIONINE (MSEm)
4n: SELENOMETHIONINE (MSEn)
4o: SELENOMETHIONINE (MSEo)
4p: SELENOMETHIONINE (MSEp)
4q: SELENOMETHIONINE (MSEq)
4r: SELENOMETHIONINE (MSEr)
4s: SELENOMETHIONINE (MSEs)
4t: SELENOMETHIONINE (MSEt)
4u: SELENOMETHIONINE (MSEu)
4v: SELENOMETHIONINE (MSEv)
4w: SELENOMETHIONINE (MSEw)
4x: SELENOMETHIONINE (MSEx)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
2
GOL
5
Ligand/Ion
GLYCEROL
3
MG
7
Ligand/Ion
MAGNESIUM ION
4
MSE
24
Mod. Amino Acid
SELENOMETHIONINE
5
SO4
8
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ILE A:113 , TYR A:135 , HIS A:136 , HOH A:231
BINDING SITE FOR RESIDUE EDO A 901
02
AC2
SOFTWARE
ALA A:88 , ALA A:90 , ILE A:95 , ASP A:121 , TRP A:125 , HOH A:246 , HOH A:469 , HOH A:724
BINDING SITE FOR RESIDUE GOL A 1001
03
AC3
SOFTWARE
THR A:118 , MSE A:119 , GLN A:120
BINDING SITE FOR RESIDUE GOL A 1002
04
AC4
SOFTWARE
ARG A:51 , PRO A:55 , HIS A:57 , ASP A:82 , HOH A:498 , HOH A:687
BINDING SITE FOR RESIDUE GOL A 1003
05
AC5
SOFTWARE
ASN A:56 , HOH A:245 , HOH A:743
BINDING SITE FOR RESIDUE EDO A 902
06
AC6
SOFTWARE
ASP A:67 , GLY A:68 , GLY A:69 , ALA A:70 , THR A:94 , ALA A:97 , HOH A:227 , HOH A:271 , ARG B:139
BINDING SITE FOR RESIDUE SO4 A 501
07
AC7
SOFTWARE
GLY A:170 , GLY A:171 , ALA A:190 , GLY A:191 , HOH A:242 , HOH A:331 , HOH A:382 , HOH A:459 , HOH A:483 , HOH A:681
BINDING SITE FOR RESIDUE SO4 A 502
08
AC8
SOFTWARE
GLU A:33 , ASP A:62 , GLU A:112 , HOH A:249 , HOH A:258 , HOH A:284 , HOH A:285
BINDING SITE FOR RESIDUE MG A 3001
09
AC9
SOFTWARE
HOH A:275 , HOH A:790 , HOH A:791 , HOH A:792 , HOH A:793 , HOH A:794
BINDING SITE FOR RESIDUE MG A 3002
10
BC1
SOFTWARE
ARG A:139 , ASP B:67 , GLY B:68 , GLY B:69 , ALA B:70 , THR B:94 , ALA B:97 , HOH B:242 , HOH B:467 , HOH B:479 , HOH B:503 , HOH B:553
BINDING SITE FOR RESIDUE SO4 B 501
11
BC2
SOFTWARE
GLY B:171 , ALA B:190 , GLY B:191 , HOH B:220 , HOH B:258 , HOH B:269 , HOH B:337 , HOH B:355 , HOH B:435
BINDING SITE FOR RESIDUE SO4 B 502
12
BC3
SOFTWARE
GLU B:33 , ASP B:62 , GLU B:112 , HOH B:239 , HOH B:249 , HOH B:302 , HOH B:304
BINDING SITE FOR RESIDUE MG B 3001
13
BC4
SOFTWARE
HIS B:52 , HOH B:531 , HOH B:774 , HOH B:775 , HOH C:266 , HOH C:505
BINDING SITE FOR RESIDUE MG B 3002
14
BC5
SOFTWARE
ALA C:88 , ALA C:90 , ILE C:92 , ILE C:95 , ASP C:121 , TRP C:125 , HOH C:264
BINDING SITE FOR RESIDUE EDO C 901
15
BC6
SOFTWARE
ARG C:212
BINDING SITE FOR RESIDUE EDO C 902
16
BC7
SOFTWARE
ASP C:67 , GLY C:68 , GLY C:69 , ALA C:70 , ALA C:93 , THR C:94 , ALA C:97 , HOH C:229 , HOH C:438 , HOH C:639 , HOH C:642 , ARG D:139
BINDING SITE FOR RESIDUE SO4 C 501
17
BC8
SOFTWARE
GLY C:170 , GLY C:171 , ALA C:190 , GLY C:191 , HOH C:217 , HOH C:396 , HOH C:474 , HOH C:500 , HOH C:694
BINDING SITE FOR RESIDUE SO4 C 502
18
BC9
SOFTWARE
THR C:13 , ASN C:14
BINDING SITE FOR RESIDUE SO4 C 503
19
CC1
SOFTWARE
HIS C:136 , HOH C:269 , HOH C:272 , HOH C:273 , HOH C:274 , HOH C:276
BINDING SITE FOR RESIDUE MG C 3002
20
CC2
SOFTWARE
GLU C:33 , ASP C:62 , GLU C:112 , HOH C:230 , HOH C:255 , HOH C:258 , HOH C:271
BINDING SITE FOR RESIDUE MG C 3001
21
CC3
SOFTWARE
ILE D:113 , TYR D:135 , HIS D:136 , SER D:138 , HOH D:221 , HOH D:231
BINDING SITE FOR RESIDUE GOL D 1001
22
CC4
SOFTWARE
ARG C:139 , HOH C:269 , ASP D:67 , GLY D:68 , GLY D:69 , ALA D:70 , THR D:94 , HOH D:708
BINDING SITE FOR RESIDUE GOL D 1002
23
CC5
SOFTWARE
ALA D:88 , ALA D:90 , TRP D:125
BINDING SITE FOR RESIDUE EDO D 901
24
CC6
SOFTWARE
GLY D:170 , GLY D:171 , ALA D:190 , GLY D:191 , HOH D:236 , HOH D:380 , HOH D:395 , HOH D:582
BINDING SITE FOR RESIDUE SO4 D 501
25
CC7
SOFTWARE
GLU D:33 , ASP D:62 , HOH D:248 , HOH D:249 , HOH D:250 , HOH D:251
BINDING SITE FOR RESIDUE MG D 3001
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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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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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3jr2a_ (A:)
1b: SCOP_d3jr2b_ (B:)
1c: SCOP_d3jr2c_ (C:)
1d: SCOP_d3jr2d_ (D:)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Ribulose-phoshate binding barrel
(356)
Family
:
automated matches
(38)
Protein domain
:
automated matches
(38)
Vibrio cholerae [TaxId: 666]
(2)
1a
d3jr2a_
A:
1b
d3jr2b_
B:
1c
d3jr2c_
C:
1d
d3jr2d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3jr2C00 (C:2-215)
1b: CATH_3jr2A00 (A:2-214)
1c: CATH_3jr2B00 (B:3-215)
1d: CATH_3jr2D00 (D:3-214)
View:
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Vibrio cholerae. Organism_taxid: 666. Strain: n16961.
(2)
1a
3jr2C00
C:2-215
1b
3jr2A00
A:2-214
1c
3jr2B00
B:3-215
1d
3jr2D00
D:3-214
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_OMPdecase_3jr2D01 (D:4-207)
1b: PFAM_OMPdecase_3jr2D02 (D:4-207)
1c: PFAM_OMPdecase_3jr2D03 (D:4-207)
1d: PFAM_OMPdecase_3jr2D04 (D:4-207)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
TIM_barrel
(694)
Family
:
OMPdecase
(84)
Vibrio cholerae
(2)
1a
OMPdecase-3jr2D01
D:4-207
1b
OMPdecase-3jr2D02
D:4-207
1c
OMPdecase-3jr2D03
D:4-207
1d
OMPdecase-3jr2D04
D:4-207
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]
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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