[English] 日本語
Yorodumi
- PDB-1v02: Crystal structure of the Sorghum bicolor dhurrinase 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v02
TitleCrystal structure of the Sorghum bicolor dhurrinase 1
Components(DHURRINASE) x 2
KeywordsHYDROLASE / BETA-GLUCOSIDASE / DHURRIN HYDROLYSIS / PEST DEFENSE / FAMILY GH1
Function / homology
Function and homology information


beta-glucosidase activity / chloroplast / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 1, active site / Glycosyl hydrolases family 1 active site. / Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesSORGHUM BICOLOR (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMoriniere, J. / Verdoucq, L. / Bevan, D.R. / Esen, A. / Henrissat, B. / Czjzek, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict ...Title: Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict Specificity, in Complex with its Natural Substrate
Authors: Verdoucq, L. / Moriniere, J. / Bevan, D.R. / Esen, A. / Vasella, A. / Henrissat, B. / Czjzek, M.
History
DepositionMar 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DHURRINASE
B: DHURRINASE
C: DHURRINASE
D: DHURRINASE
E: DHURRINASE
F: DHURRINASE


Theoretical massNumber of molelcules
Total (without water)383,6196
Polymers383,6196
Non-polymers00
Water91,3005068
1
A: DHURRINASE
B: DHURRINASE


Theoretical massNumber of molelcules
Total (without water)127,8642
Polymers127,8642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DHURRINASE
D: DHURRINASE


Theoretical massNumber of molelcules
Total (without water)127,8642
Polymers127,8642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: DHURRINASE
F: DHURRINASE


Theoretical massNumber of molelcules
Total (without water)127,8922
Polymers127,8922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.050, 101.050, 279.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLEULEU6AA13 - 3064 - 81
21ARGARGLEULEU6BB13 - 3064 - 81
31ARGARGLEULEU6CC13 - 3064 - 81
41ARGARGLEULEU6DD13 - 3064 - 81
51ARGARGLEULEU6EE13 - 3064 - 81
61ARGARGLEULEU6FF13 - 3064 - 81
12LEULEUASNASN1AA30 - 6081 - 111
22LEULEUASNASN1BB30 - 6081 - 111
32LEULEUASNASN1CC30 - 6081 - 111
42LEULEUASNASN1DD30 - 6081 - 111
52LEULEUASNASN1EE30 - 6081 - 111
62LEULEUASNASN1FF30 - 6081 - 111
13PHEPHEVALVAL6AA61 - 85112 - 136
23PHEPHEVALVAL6BB61 - 85112 - 136
33PHEPHEVALVAL6CC61 - 85112 - 136
43PHEPHEVALVAL6DD61 - 85112 - 136
53PHEPHEVALVAL6EE61 - 85112 - 136
63PHEPHEVALVAL6FF61 - 85112 - 136
14ARGARGASNASN1AA86 - 116137 - 167
24ARGARGASNASN1BB86 - 116137 - 167
34ARGARGASNASN1CC86 - 116137 - 167
44ARGARGASNASN1DD86 - 116137 - 167
54ARGARGASNASN1EE86 - 116137 - 167
64ARGARGASNASN1FF86 - 116137 - 167
15GLUGLUILEILE6AA117 - 139168 - 190
25GLUGLUILEILE6BB117 - 139168 - 190
35GLUGLUILEILE6CC117 - 139168 - 190
45GLUGLUILEILE6DD117 - 139168 - 190
55GLUGLUILEILE6EE117 - 139168 - 190
65GLUGLUILEILE6FF117 - 139168 - 190
16THRTHRPHEPHE1AA140 - 157191 - 208
26THRTHRPHEPHE1BB140 - 157191 - 208
36THRTHRPHEPHE1CC140 - 157191 - 208
46THRTHRPHEPHE1DD140 - 157191 - 208
56THRTHRPHEPHE1EE140 - 157191 - 208
66THRTHRPHEPHE1FF140 - 157191 - 208
17LEULEUTHRTHR6AA158 - 180209 - 231
27LEULEUTHRTHR6BB158 - 180209 - 231
37LEULEUTHRTHR6CC158 - 180209 - 231
47LEULEUTHRTHR6DD158 - 180209 - 231
57LEULEULYSLYS6EE158 - 180209 - 231
67LEULEUTHRTHR6FF158 - 180209 - 231
18VALVALLEULEU1AA181 - 203232 - 254
28VALVALLEULEU1BB181 - 203232 - 254
38VALVALLEULEU1CC181 - 203232 - 254
48VALVALLEULEU1DD181 - 203232 - 254
58VALVALLEULEU1EE181 - 203232 - 254
68VALVALLEULEU1FF181 - 203232 - 254
19ALAALAGLUGLU6AA204 - 238255 - 289
29ALAALAGLUGLU6BB204 - 238255 - 289
39ALAALAGLUGLU6CC204 - 238255 - 289
49ALAALAGLUGLU6DD204 - 238255 - 289
59ALAALAGLUGLU6EE204 - 238255 - 289
69ALAALAGLUGLU6FF204 - 238255 - 289
110THRTHRGLNGLN1AA239 - 273290 - 324
210THRTHRGLNGLN1BB239 - 273290 - 324
310THRTHRGLNGLN1CC239 - 273290 - 324
410THRTHRGLNGLN1DD239 - 273290 - 324
510THRTHRGLNGLN1EE239 - 273290 - 324
610THRTHRGLNGLN1FF239 - 273290 - 324
111GLNGLNLEULEU6AA274 - 284325 - 335
211GLNGLNLEULEU6BB274 - 284325 - 335
311GLNGLNLEULEU6CC274 - 284325 - 335
411GLNGLNLEULEU6DD274 - 284325 - 335
511GLNGLNLEULEU6EE274 - 284325 - 335
611GLNGLNLEULEU6FF274 - 284325 - 335
112GLYGLYASPASP1AA285 - 352336 - 403
212GLYGLYASPASP1BB285 - 352336 - 403
312GLYGLYASPASP1CC285 - 352336 - 403
412GLYGLYASPASP1DD285 - 352336 - 403
512GLYGLYASPASP1EE285 - 352336 - 403
612GLYGLYASPASP1FF285 - 352336 - 403
113ASPASPLEULEU6AA353 - 388404 - 439
213ASPASPLEULEU6BB353 - 388404 - 439
313ASPASPLEULEU6CC353 - 388404 - 439
413ASPASPLEULEU6DD353 - 388404 - 439
513ASPASPLEULEU6EE353 - 388404 - 439
613ASPASPLEULEU6FF353 - 388404 - 439
114METMETGLYGLY1AA389 - 406440 - 457
214METMETGLYGLY1BB389 - 406440 - 457
314METMETGLYGLY1CC389 - 406440 - 457
414METMETGLYGLY1DD389 - 406440 - 457
514METMETGLYGLY1EE389 - 406440 - 457
614METMETGLYGLY1FF389 - 406440 - 457
115METMETLYSLYS6AA407 - 438458 - 489
215METMETLYSLYS6BB407 - 438458 - 489
315METMETLYSLYS6CC407 - 438458 - 489
415METMETLYSLYS6DD407 - 438458 - 489
515METMETLYSLYS6EE407 - 438458 - 489
615METMETLYSLYS6FF407 - 438458 - 489
116GLNGLNTYRTYR1AA439 - 450490 - 501
216GLNGLNTYRTYR1BB439 - 450490 - 501
316GLNGLNTYRTYR1CC439 - 450490 - 501
416GLNGLNTYRTYR1DD439 - 450490 - 501
516GLNGLNTYRTYR1EE439 - 450490 - 501
616GLNGLNTYRTYR1FF439 - 450490 - 501
117PHEPHEGLYGLY6AA451 - 496502 - 547
217PHEPHEGLYGLY6BB451 - 496502 - 547
317PHEPHEGLYGLY6CC451 - 496502 - 547
417PHEPHEGLYGLY6DD451 - 496502 - 547
517PHEPHEGLYGLY6EE451 - 496502 - 547
617PHEPHEGLYGLY6FF451 - 496502 - 547

NCS oper:
IDCodeMatrixVector
1given(0.22732, -0.97175, -0.0635), (-0.97267, -0.22974, 0.03358), (-0.04722, 0.05413, -0.99742)38.58124, 51.77372, -50.34843
2given(-0.49992, -0.86336, 0.06842), (0.86395, -0.50267, -0.03035), (0.0606, 0.04394, 0.99719)1.06223, 113.64437, -2.26259
3given(0.72873, 0.68113, -0.07079), (0.68013, -0.73193, -0.04116), (-0.07985, -0.01815, -0.99664)-66.11475, 122.87324, -47.93115
4given(-0.49704, 0.8654, 0.06353), (-0.86624, -0.49914, 0.0221), (0.05084, -0.04404, 0.99774)3.23123, 57.63508, 0.00199
5given(-0.95467, 0.29743, -0.01159), (0.29739, 0.95474, 0.00509), (0.01258, 0.00141, -0.99992)25.13749, -3.08495, -49.70576

-
Components

#1: Protein
DHURRINASE / DHURRINASE-1


Mass: 63931.754 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SORGHUM BICOLOR (sorghum) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q41290, beta-glucosidase
#2: Protein DHURRINASE / DHURRINASE-1


Mass: 63959.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SORGHUM BICOLOR (sorghum) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q41290, beta-glucosidase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5068 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.593 Å3/Da / Density % sol: 52 %
Crystal growpH: 7 / Details: 16% PEG-MONO-METHYL-ETHER 2000, 0.1 M TRIS PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Jan 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→39 Å / Num. obs: 291187 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.1 / % possible all: 89.6

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E1E

1e1e


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.419 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21 14720 5.1 %RANDOM
Rwork0.172 ---
obs0.173 276371 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å20 Å2
2--0.89 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23259 0 0 5068 28327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02123955
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.93732548
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71752898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.23318
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218851
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.313101
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2750.56568
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.3151
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.5241
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.089214431
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.854323246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.57229524
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.34939302
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1883tight positional0.070.05
2B1883tight positional0.050.05
3C1883tight positional0.10.05
4D1883tight positional0.050.05
5E1883tight positional0.080.05
6F1883tight positional0.070.05
1A1989loose positional0.255
2B1989loose positional0.45
3C1989loose positional0.415
4D1989loose positional0.245
5E1989loose positional0.355
6F1989loose positional0.325
1A1883tight thermal0.20.5
2B1883tight thermal0.190.5
3C1883tight thermal0.20.5
4D1883tight thermal0.210.5
5E1883tight thermal0.210.5
6F1883tight thermal0.20.5
1A1989loose thermal1.710
2B1989loose thermal1.4110
3C1989loose thermal1.6710
4D1989loose thermal1.5210
5E1989loose thermal1.5510
6F1989loose thermal1.9910
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 969
Rwork0.263 18302

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more