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Biol. Unit 3
Info
Asym.Unit (351 KB)
Biol.Unit 1 (177 KB)
Biol.Unit 2 (176 KB)
Biol.Unit 3 (344 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF GH78 FAMILY RHAMNOSIDASE OF BACILLUS SP. GL1 AT 1.9 A
Authors
:
Z. Cui, B. Mikami, W. Hashimoto, K. Murata
Date
:
17 Jan 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Alpha Barrel, Rhamnosidase, Glycoside Hydrolase Family 78, Invertase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Cui, Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata
Crystal Structure Of Glycoside Hydrolase Family 78 Alpha-L-Rhamnosidase From Bacillus Sp. Gl1
J. Mol. Biol. V. 374 384 2007
[
close entry info
]
Hetero Components
(1, 43)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2aa: GLYCEROL (GOLaa)
2ab: GLYCEROL (GOLab)
2ac: GLYCEROL (GOLac)
2ad: GLYCEROL (GOLad)
2ae: GLYCEROL (GOLae)
2af: GLYCEROL (GOLaf)
2ag: GLYCEROL (GOLag)
2ah: GLYCEROL (GOLah)
2ai: GLYCEROL (GOLai)
2aj: GLYCEROL (GOLaj)
2ak: GLYCEROL (GOLak)
2al: GLYCEROL (GOLal)
2am: GLYCEROL (GOLam)
2an: GLYCEROL (GOLan)
2ao: GLYCEROL (GOLao)
2ap: GLYCEROL (GOLap)
2aq: GLYCEROL (GOLaq)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
2z: GLYCEROL (GOLz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
43
Ligand/Ion
GLYCEROL
[
close Hetero Component info
]
Sites
(47, 47)
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)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:423 , HIS A:522 , GOL A:3040 , HOH A:4755 , HOH A:4756 , HOH A:4757
BINDING SITE FOR RESIDUE CA A 4001
02
AC2
SOFTWARE
GLU A:946 , LYS B:953 , GOL B:3041 , HOH B:4705 , HOH B:4874 , HOH B:4875
BINDING SITE FOR RESIDUE CA B 4002
03
AC3
SOFTWARE
VAL B:423 , HIS B:522 , GOL B:3042 , HOH B:4700 , HOH B:4701 , HOH B:4702
BINDING SITE FOR RESIDUE CA B 4003
04
AC4
SOFTWARE
LYS A:953 , GOL A:3039 , GOL A:3043 , GLU B:946 , HOH B:4704
BINDING SITE FOR RESIDUE CA A 4004
05
AC5
SOFTWARE
GLN A:58 , VAL A:59 , GLY A:60 , GLU A:200 , ARG A:527 , HOH A:4582 , HOH A:4589
BINDING SITE FOR RESIDUE GOL A 3001
06
AC6
SOFTWARE
TRP A:163 , TYR A:497 , VAL A:498 , HOH A:4587 , HOH A:4835
BINDING SITE FOR RESIDUE GOL A 3002
07
AC7
SOFTWARE
PHE A:262 , GLY A:265 , VAL A:266 , ARG A:267 , SER A:314 , HIS A:315 , PHE A:316 , HOH A:4466
BINDING SITE FOR RESIDUE GOL A 3003
08
AC8
SOFTWARE
TRP A:403 , HOH A:4267 , HOH A:4606
BINDING SITE FOR RESIDUE GOL A 3004
09
AC9
SOFTWARE
GLN B:58 , VAL B:59 , GLY B:60 , GLU B:200 , ARG B:527 , HOH B:4413
BINDING SITE FOR RESIDUE GOL B 3005
10
BC1
SOFTWARE
SER A:542 , TRP A:900 , HOH A:4111 , HOH A:4317 , HOH A:4736 , HOH A:4737 , LEU B:545 , GLY B:829
BINDING SITE FOR RESIDUE GOL A 3006
11
BC2
SOFTWARE
ASP A:567 , GLU A:572 , TRP A:576 , ASP A:579 , TRP A:629 , GLU A:841 , ARG A:858 , HIS A:862 , TRP A:864 , HOH A:4018
BINDING SITE FOR RESIDUE GOL A 3007
12
BC3
SOFTWARE
MET A:764 , GLN A:797 , ILE A:798 , ASP A:823 , ARG A:826 , ASN A:827 , GOL A:3019
BINDING SITE FOR RESIDUE GOL A 3008
13
BC4
SOFTWARE
LEU A:545 , GLY A:829 , SER B:542 , TRP B:900 , HOH B:4422
BINDING SITE FOR RESIDUE GOL B 3009
14
BC5
SOFTWARE
TRP B:163 , TYR B:497 , VAL B:498 , HOH B:4254 , HOH B:4449 , HOH B:4611 , HOH B:4727
BINDING SITE FOR RESIDUE GOL B 3010
15
BC6
SOFTWARE
ILE B:798 , ASN B:827 , GLN B:830 , TYR B:843 , GOL B:3020 , HOH B:4574 , HOH B:4793
BINDING SITE FOR RESIDUE GOL B 3011
16
BC7
SOFTWARE
LEU B:223 , GLY B:265 , VAL B:266 , ARG B:267 , SER B:314 , HIS B:315 , PHE B:316 , HOH B:4317
BINDING SITE FOR RESIDUE GOL B 3012
17
BC8
SOFTWARE
TRP B:403 , HOH B:4304 , HOH B:4503
BINDING SITE FOR RESIDUE GOL B 3013
18
BC9
SOFTWARE
ASP B:567 , GLU B:572 , TRP B:576 , ASP B:579 , TRP B:629 , ARG B:858 , HIS B:862 , TRP B:864 , GOL B:3025 , HOH B:4097
BINDING SITE FOR RESIDUE GOL B 3014
19
CC1
SOFTWARE
THR A:279 , GLU A:280 , TRP A:281 , HOH A:4703
BINDING SITE FOR RESIDUE GOL A 3015
20
CC2
SOFTWARE
THR B:279 , GLU B:280 , TRP B:281 , HOH B:4713
BINDING SITE FOR RESIDUE GOL B 3016
21
CC3
SOFTWARE
TYR A:245 , TYR A:364 , ARG A:365 , PRO A:368 , GLU A:369 , HOH A:4849
BINDING SITE FOR RESIDUE GOL A 3017
22
CC4
SOFTWARE
TYR B:245 , SER B:269 , TYR B:364 , ARG B:365 , PRO B:368 , GLU B:369
BINDING SITE FOR RESIDUE GOL B 3018
23
CC5
SOFTWARE
ILE A:798 , ARG A:826 , ASN A:827 , GLN A:830 , TYR A:843 , PHE A:846 , GOL A:3008 , HOH A:4808
BINDING SITE FOR RESIDUE GOL A 3019
24
CC6
SOFTWARE
MET B:764 , GLN B:797 , ILE B:798 , ASP B:823 , ARG B:826 , ASN B:827 , GOL B:3011 , HOH B:4095
BINDING SITE FOR RESIDUE GOL B 3020
25
CC7
SOFTWARE
GLU A:425 , SER B:75 , ARG B:193 , ILE B:195 , PHE B:197 , HOH B:4204 , HOH B:4720
BINDING SITE FOR RESIDUE GOL B 3021
26
CC8
SOFTWARE
SER A:75 , ARG A:193 , ILE A:195 , PRO A:196 , PHE A:197 , HOH A:4109 , HOH A:4665 , GLU B:425
BINDING SITE FOR RESIDUE GOL A 3022
27
CC9
SOFTWARE
GLU A:201 , HOH A:4113 , TYR B:204 , PRO B:205 , HOH B:4132
BINDING SITE FOR RESIDUE GOL A 3023
28
DC1
SOFTWARE
PRO A:205 , ALA A:206 , GLU B:201 , GLN B:528 , ARG B:558 , HOH B:4124 , HOH B:4403
BINDING SITE FOR RESIDUE GOL B 3024
29
DC2
SOFTWARE
PHE B:102 , GLN B:147 , GLU B:572 , TRP B:576 , ASN B:849 , ARG B:858 , GOL B:3014
BINDING SITE FOR RESIDUE GOL B 3025
30
DC3
SOFTWARE
GLN A:147 , GLU A:572 , TRP A:679 , TRP A:684 , HOH A:4863
BINDING SITE FOR RESIDUE GOL A 3026
31
DC4
SOFTWARE
GLU A:70 , VAL A:191 , ASP A:194 , ASN A:602 , HOH A:4097 , HOH A:4326 , HOH A:4439 , HOH A:4620
BINDING SITE FOR RESIDUE GOL A 3027
32
DC5
SOFTWARE
GLU B:70 , VAL B:191 , ASN B:602 , HOH B:4238
BINDING SITE FOR RESIDUE GOL B 3028
33
DC6
SOFTWARE
GLY B:28 , SER B:29 , ALA B:128 , ARG B:130 , HOH B:4877
BINDING SITE FOR RESIDUE GOL B 3029
34
DC7
SOFTWARE
GLY A:28 , SER A:29 , ALA A:128 , HOH A:4391 , HOH A:4760
BINDING SITE FOR RESIDUE GOL A 3030
35
DC8
SOFTWARE
ARG A:157
BINDING SITE FOR RESIDUE GOL A 3031
36
DC9
SOFTWARE
ARG A:327 , ARG B:157 , GLU B:158 , LEU B:159 , ARG B:491 , HOH B:4849
BINDING SITE FOR RESIDUE GOL B 3032
37
EC1
SOFTWARE
ARG A:213 , ARG A:410 , PHE A:432 , GLU A:433 , ASP A:434 , HOH A:4854
BINDING SITE FOR RESIDUE GOL A 3033
38
EC2
SOFTWARE
ARG B:213 , ARG B:410 , PHE B:432 , GLU B:433 , ASP B:434 , HOH B:4878
BINDING SITE FOR RESIDUE GOL B 3034
39
EC3
SOFTWARE
ARG A:447 , GLU A:551 , HIS A:555 , ARG A:558 , HOH A:4134
BINDING SITE FOR RESIDUE GOL A 3035
40
EC4
SOFTWARE
ARG B:447 , HIS B:555 , HOH B:4092 , HOH B:4105
BINDING SITE FOR RESIDUE GOL B 3036
41
EC5
SOFTWARE
PHE B:631 , ILE B:634 , LEU B:635 , PHE B:701 , LYS B:704 , ALA B:705 , ASP B:708
BINDING SITE FOR RESIDUE GOL B 3037
42
EC6
SOFTWARE
PRO A:353 , THR B:342 , LYS B:385 , HOH B:4489 , HOH B:4514
BINDING SITE FOR RESIDUE GOL B 3038
43
EC7
SOFTWARE
GLU A:933 , LYS A:953 , TYR A:954 , GOL A:3043 , CA A:4004 , GLU B:946 , HOH B:4392
BINDING SITE FOR RESIDUE GOL A 3039
44
EC8
SOFTWARE
VAL A:423 , PRO A:424 , HIS A:522 , GLU A:523 , CA A:4001 , HOH A:4506 , HOH A:4507
BINDING SITE FOR RESIDUE GOL A 3040
45
EC9
SOFTWARE
GLU A:946 , HOH A:4569 , GLU B:933 , LYS B:953 , TYR B:954 , MET B:955 , CA B:4002 , HOH B:4714 , HOH B:4802 , HOH B:4874
BINDING SITE FOR RESIDUE GOL B 3041
46
FC1
SOFTWARE
VAL B:423 , PRO B:424 , HIS B:522 , GLU B:523 , CA B:4003 , HOH B:4160 , HOH B:4701
BINDING SITE FOR RESIDUE GOL B 3042
47
FC2
SOFTWARE
VAL A:952 , LYS A:953 , TYR A:954 , GOL A:3039 , CA A:4004 , HOH A:4580 , HOH A:4812 , GLU B:946 , HOH B:4704
BINDING SITE FOR RESIDUE GOL A 3043
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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Note:
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
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Bac_rhamnosid_2okxB01 (B:431-941)
1b: PFAM_Bac_rhamnosid_2okxB02 (B:431-941)
2a: PFAM_Bac_rhamnosid_N_2okxB03 (B:35-210)
2b: PFAM_Bac_rhamnosid_N_2okxB04 (B:35-210)
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(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
Bac_rhamnosid
(1)
Bacillus sp. (strain GL1)
(1)
1a
Bac_rhamnosid-2okxB01
B:431-941
1b
Bac_rhamnosid-2okxB02
B:431-941
Clan
:
GBD
(153)
Family
:
Bac_rhamnosid_N
(1)
Bacillus sp. (strain GL1)
(1)
2a
Bac_rhamnosid_N-2okxB03
B:35-210
2b
Bac_rhamnosid_N-2okxB04
B:35-210
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