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2R8Z
Asym. Unit
Info
Asym.Unit (493 KB)
Biol.Unit 1 (239 KB)
Biol.Unit 2 (252 KB)
Biol.Unit 3 (131 KB)
Biol.Unit 4 (124 KB)
Biol.Unit 5 (130 KB)
Biol.Unit 6 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YRBI PHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH A PHOSPHATE AND A CALCIUM ION
Authors
:
O. V. Tsodikov, P. Aggarwal, J. R. Rubin, J. A. Stuckey, R. W. Woodard, T.
Date
:
11 Sep 07 (Deposition) - 23 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: I,J,K,L,M,N,O,P (1x)
Biol. Unit 2: A,B,C,D,E,F,G,H (1x)
Biol. Unit 3: A,B,C,D (1x)
Biol. Unit 4: I,J,K,L (1x)
Biol. Unit 5: E,F,G,H (1x)
Biol. Unit 6: M,N,O,P (1x)
Keywords
:
Yrbi, Phosphatase, Divalent Metal, Phosphate, Kdo8-P, Had Superfamily, Hydrolase, Lipopolysaccharide Biosynthesis, Magnesium
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Biswas, L. Yi, P. Aggarwal, J. Wu, J. R. Rubin, J. A. Stuckey, R. W. Woodard, O. V. Tsodikov
The Tail Of Kdsc: Conformational Changes Control The Activity Of A Haloacid Dehalogenase Superfamily Phosphatase
J. Biol. Chem. V. 284 30594 2009
[
close entry info
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Hetero Components
(2, 32)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
2a: PHOSPHATE ION (PO4a)
2b: PHOSPHATE ION (PO4b)
2c: PHOSPHATE ION (PO4c)
2d: PHOSPHATE ION (PO4d)
2e: PHOSPHATE ION (PO4e)
2f: PHOSPHATE ION (PO4f)
2g: PHOSPHATE ION (PO4g)
2h: PHOSPHATE ION (PO4h)
2i: PHOSPHATE ION (PO4i)
2j: PHOSPHATE ION (PO4j)
2k: PHOSPHATE ION (PO4k)
2l: PHOSPHATE ION (PO4l)
2m: PHOSPHATE ION (PO4m)
2n: PHOSPHATE ION (PO4n)
2o: PHOSPHATE ION (PO4o)
2p: PHOSPHATE ION (PO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
16
Ligand/Ion
CALCIUM ION
2
PO4
16
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
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Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:32 , ASP A:34 , ASP A:125 , PO4 A:202 , HOH A:203 , HOH A:204
BINDING SITE FOR RESIDUE CA A 201
02
AC2
SOFTWARE
HOH A:302 , ASP B:32 , ASP B:34 , ASP B:125 , PO4 B:203 , HOH B:205
BINDING SITE FOR RESIDUE CA B 202
03
AC3
SOFTWARE
ASP C:32 , ASP C:34 , ASP C:125 , PO4 C:204 , HOH C:205 , HOH C:206
BINDING SITE FOR RESIDUE CA C 203
04
AC4
SOFTWARE
HOH C:207 , ASP D:32 , ASP D:34 , ASP D:125 , PO4 D:205 , HOH D:209
BINDING SITE FOR RESIDUE CA D 204
05
AC5
SOFTWARE
ASP E:32 , ASP E:34 , ASP E:125 , PO4 E:206 , HOH E:208 , HOH H:210
BINDING SITE FOR RESIDUE CA E 205
06
AC6
SOFTWARE
ASP F:32 , ASP F:34 , ASP F:125 , PO4 F:207 , HOH F:238 , HOH F:252
BINDING SITE FOR RESIDUE CA F 206
07
AC7
SOFTWARE
ASP G:32 , ASP G:34 , ASP G:125 , PO4 G:208 , HOH G:210 , HOH G:400
BINDING SITE FOR RESIDUE CA G 207
08
AC8
SOFTWARE
HOH G:212 , ASP H:32 , ASP H:34 , ASP H:125 , PO4 H:209 , HOH H:211
BINDING SITE FOR RESIDUE CA H 208
09
AC9
SOFTWARE
ASP I:32 , ASP I:34 , ASP I:125 , PO4 I:210 , HOH I:211 , HOH I:270
BINDING SITE FOR RESIDUE CA I 209
10
BC1
SOFTWARE
ASP J:32 , ASP J:34 , ASP J:125 , PO4 J:211 , HOH J:309
BINDING SITE FOR RESIDUE CA J 210
11
BC2
SOFTWARE
ASP K:32 , ASP K:34 , ASP K:125 , PO4 K:212 , HOH K:213
BINDING SITE FOR RESIDUE CA K 211
12
BC3
SOFTWARE
ASP L:32 , ASP L:34 , ASP L:125 , PO4 L:213 , HOH L:215
BINDING SITE FOR RESIDUE CA L 212
13
BC4
SOFTWARE
ASP M:32 , ASP M:34 , ASP M:125 , PO4 M:214 , HOH M:277 , HOH M:329
BINDING SITE FOR RESIDUE CA M 213
14
BC5
SOFTWARE
HOH M:221 , ASP N:32 , ASP N:34 , ASP N:125 , PO4 N:215 , HOH N:217
BINDING SITE FOR RESIDUE CA N 214
15
BC6
SOFTWARE
ASP O:32 , ASP O:34 , ASP O:125 , PO4 O:216 , HOH O:221 , HOH O:222
BINDING SITE FOR RESIDUE CA O 215
16
BC7
SOFTWARE
ASP P:32 , ASP P:34 , ASP P:125 , PO4 P:217 , HOH P:218 , HOH P:299
BINDING SITE FOR RESIDUE CA P 216
17
BC8
SOFTWARE
ASP A:32 , VAL A:33 , ASP A:34 , THR A:76 , GLY A:77 , LYS A:102 , CA A:201 , HOH A:203 , HOH A:204 , HOH A:205 , SER D:187
BINDING SITE FOR RESIDUE PO4 A 202
18
BC9
SOFTWARE
SER A:187 , ASP B:32 , VAL B:33 , ASP B:34 , THR B:76 , GLY B:77 , LYS B:102 , CA B:202 , HOH B:206
BINDING SITE FOR RESIDUE PO4 B 203
19
CC1
SOFTWARE
SER B:187 , HOH B:207 , ASP C:32 , VAL C:33 , ASP C:34 , THR C:76 , GLY C:77 , LYS C:102 , CA C:203 , HOH C:205 , HOH C:206
BINDING SITE FOR RESIDUE PO4 C 204
20
CC2
SOFTWARE
SER C:187 , ASP D:32 , VAL D:33 , ASP D:34 , THR D:76 , GLY D:77 , LYS D:102 , CA D:204 , HOH D:209 , HOH D:210
BINDING SITE FOR RESIDUE PO4 D 205
21
CC3
SOFTWARE
ASP E:32 , VAL E:33 , ASP E:34 , THR E:76 , GLY E:77 , LYS E:102 , CA E:205 , HOH E:208 , HOH E:209 , SER H:187
BINDING SITE FOR RESIDUE PO4 E 206
22
CC4
SOFTWARE
ASP F:32 , VAL F:33 , ASP F:34 , THR F:76 , GLY F:77 , LYS F:102 , CA F:206 , HOH F:238 , HOH F:374
BINDING SITE FOR RESIDUE PO4 F 207
23
CC5
SOFTWARE
SER F:187 , ASP G:32 , VAL G:33 , ASP G:34 , THR G:76 , GLY G:77 , ARG G:78 , LYS G:102 , CA G:207 , HOH G:210 , HOH G:211 , HOH G:400
BINDING SITE FOR RESIDUE PO4 G 208
24
CC6
SOFTWARE
SER G:187 , ASP H:32 , VAL H:33 , ASP H:34 , THR H:76 , GLY H:77 , LYS H:102 , CA H:208 , HOH H:212
BINDING SITE FOR RESIDUE PO4 H 209
25
CC7
SOFTWARE
ASP I:32 , VAL I:33 , ASP I:34 , THR I:76 , GLY I:77 , ARG I:78 , LYS I:102 , CA I:209 , HOH I:270 , SER L:187
BINDING SITE FOR RESIDUE PO4 I 210
26
CC8
SOFTWARE
SER I:187 , ASP J:32 , VAL J:33 , ASP J:34 , THR J:76 , GLY J:77 , ARG J:78 , LYS J:102 , CA J:210 , HOH J:212
BINDING SITE FOR RESIDUE PO4 J 211
27
CC9
SOFTWARE
SER J:187 , ASP K:32 , VAL K:33 , ASP K:34 , THR K:76 , GLY K:77 , ARG K:78 , LYS K:102 , CA K:211 , HOH K:294
BINDING SITE FOR RESIDUE PO4 K 212
28
DC1
SOFTWARE
SER K:187 , ASP L:32 , VAL L:33 , ASP L:34 , THR L:76 , GLY L:77 , LYS L:102 , CA L:212 , HOH L:214
BINDING SITE FOR RESIDUE PO4 L 213
29
DC2
SOFTWARE
ASP M:32 , VAL M:33 , ASP M:34 , THR M:76 , GLY M:77 , ARG M:78 , LYS M:102 , CA M:213 , HOH M:329
BINDING SITE FOR RESIDUE PO4 M 214
30
DC3
SOFTWARE
SER M:187 , HOH M:221 , ASP N:32 , VAL N:33 , ASP N:34 , THR N:76 , GLY N:77 , ARG N:78 , LYS N:102 , CA N:214 , HOH N:218
BINDING SITE FOR RESIDUE PO4 N 215
31
DC4
SOFTWARE
ASP O:32 , VAL O:33 , ASP O:34 , THR O:76 , GLY O:77 , ARG O:78 , LYS O:102 , CA O:215 , HOH O:221 , HOH O:223
BINDING SITE FOR RESIDUE PO4 O 216
32
DC5
SOFTWARE
ASP P:32 , VAL P:33 , ASP P:34 , THR P:76 , GLY P:77 , ARG P:78 , LYS P:102 , CA P:216 , HOH P:299 , HOH P:329
BINDING SITE FOR RESIDUE PO4 P 217
[
close Site info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d2r8za_ (A:)
1b: SCOP_d2r8zc_ (C:)
1c: SCOP_d2r8zd_ (D:)
1d: SCOP_d2r8ze_ (E:)
1e: SCOP_d2r8zf_ (F:)
1f: SCOP_d2r8zg_ (G:)
1g: SCOP_d2r8zh_ (H:)
1h: SCOP_d2r8zi_ (I:)
1i: SCOP_d2r8zj_ (J:)
1j: SCOP_d2r8zk_ (K:)
1k: SCOP_d2r8zl_ (L:)
1l: SCOP_d2r8zm_ (M:)
1m: SCOP_d2r8zn_ (N:)
1n: SCOP_d2r8zo_ (O:)
1o: SCOP_d2r8zp_ (P:)
1p: SCOP_d2r8zb_ (B:)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
automated matches
(99)
Protein domain
:
automated matches
(99)
Escherichia coli [TaxId: 217992]
(2)
1a
d2r8za_
A:
1b
d2r8zc_
C:
1c
d2r8zd_
D:
1d
d2r8ze_
E:
1e
d2r8zf_
F:
1f
d2r8zg_
G:
1g
d2r8zh_
H:
1h
d2r8zi_
I:
1i
d2r8zj_
J:
1j
d2r8zk_
K:
1k
d2r8zl_
L:
1l
d2r8zm_
M:
1m
d2r8zn_
N:
1n
d2r8zo_
O:
1o
d2r8zp_
P:
1p
d2r8zb_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Hydrolase_3_2r8zP01 (P:88-167)
1b: PFAM_Hydrolase_3_2r8zP02 (P:88-167)
1c: PFAM_Hydrolase_3_2r8zP03 (P:88-167)
1d: PFAM_Hydrolase_3_2r8zP04 (P:88-167)
1e: PFAM_Hydrolase_3_2r8zP05 (P:88-167)
1f: PFAM_Hydrolase_3_2r8zP06 (P:88-167)
1g: PFAM_Hydrolase_3_2r8zP07 (P:88-167)
1h: PFAM_Hydrolase_3_2r8zP08 (P:88-167)
1i: PFAM_Hydrolase_3_2r8zP09 (P:88-167)
1j: PFAM_Hydrolase_3_2r8zP10 (P:88-167)
1k: PFAM_Hydrolase_3_2r8zP11 (P:88-167)
1l: PFAM_Hydrolase_3_2r8zP12 (P:88-167)
1m: PFAM_Hydrolase_3_2r8zP13 (P:88-167)
1n: PFAM_Hydrolase_3_2r8zP14 (P:88-167)
1o: PFAM_Hydrolase_3_2r8zP15 (P:88-167)
1p: PFAM_Hydrolase_3_2r8zP16 (P:88-167)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase_3
(28)
Escherichia coli O6
(4)
1a
Hydrolase_3-2r8zP01
P:88-167
1b
Hydrolase_3-2r8zP02
P:88-167
1c
Hydrolase_3-2r8zP03
P:88-167
1d
Hydrolase_3-2r8zP04
P:88-167
1e
Hydrolase_3-2r8zP05
P:88-167
1f
Hydrolase_3-2r8zP06
P:88-167
1g
Hydrolase_3-2r8zP07
P:88-167
1h
Hydrolase_3-2r8zP08
P:88-167
1i
Hydrolase_3-2r8zP09
P:88-167
1j
Hydrolase_3-2r8zP10
P:88-167
1k
Hydrolase_3-2r8zP11
P:88-167
1l
Hydrolase_3-2r8zP12
P:88-167
1m
Hydrolase_3-2r8zP13
P:88-167
1n
Hydrolase_3-2r8zP14
P:88-167
1o
Hydrolase_3-2r8zP15
P:88-167
1p
Hydrolase_3-2r8zP16
P:88-167
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