[English] 日本語
Yorodumi
- PDB-4gzj: Active-site mutant of potato endo-1,3-beta-glucanase in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gzj
TitleActive-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose and laminaratetrose
ComponentsGlucan endo-1,3-beta-D-glucosidase
KeywordsHYDROLASE / glucoside hydrolase / GH17 family / pathogenesis-related class-2 protein (PR-2) / carbohydrate/sugar binding / catalytic nucleophile mutation / laminaratriose / laminaratetrose / TIM Barrel
Function / homology
Function and homology information


glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / defense response / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 17, plant / Glycosyl hydrolases family 17 signature. / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-laminaribiose / 1,3-beta-D-glucan glucanohydrolase (Glucan endo-1,3-beta-glucosidase a)
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structures of an active-site mutant of a plant 1,3-beta-glucanase in complex with oligosaccharide products of hydrolysis
Authors: Wojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Two high-resolution crystal structures of potato 1,3-beta-glucanase reveal subdomain flexibility with implications for substrate binding
Authors: Wojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Three-dimensional structures of two plant beta-glucan endohydrolases with distinct substrate specificities.
Authors: Varghese, J.N. / Garrett, T.P. / Colman, P.M. / Chen, L. / H j, P.B. / Fincher, G.B. / Peumans, W.J.
#3: Journal: Proteins / Year: 2006
Title: Crystal structure at 1.45-A resolution of the major allergen endo-beta-1,3-glucanase of banana as a molecular basis for the latex-fruit syndrome.
Authors: Receveur-Br chot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J. / Roug, P.
History
DepositionSep 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 2, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucan endo-1,3-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3983
Polymers36,5511
Non-polymers8472
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.307, 49.202, 57.431
Angle α, β, γ (deg.)90.00, 98.84, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Glucan endo-1,3-beta-D-glucosidase / 1 / 3-beta-D-glucan glucanohydrolase


Mass: 36550.934 Da / Num. of mol.: 1
Fragment: mature endo-1,3-beta-glucanase, UNP residues 24-338
Mutation: E259A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Strain: DESIREE / Gene: glub20-2 / Plasmid: pET-30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21
References: UniProt: Q70C53, glucan endo-1,3-beta-D-glucosidase
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-laminaribiose
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate, 0.2 M ammonium acetate, 24% PEG 8000, 0.4 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Feb 4, 2007 / Details: mirrors
RadiationMonochromator: Ge(111) triangular bent crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.55→40 Å / Num. all: 44391 / Num. obs: 44391 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.3
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4390 / % possible all: 100

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4GZI

4gzi


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.569 / SU ML: 0.049 / Isotropic thermal model: Isotropic / Cross valid method: R-FREE / σ(I): -3 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 1139 2.6 %RANDOM
Rwork0.1507 ---
all0.1515 43213 --
obs0.1515 43213 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.47 Å2
2---0.49 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 57 356 2922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222653
X-RAY DIFFRACTIONr_bond_other_d0.0010.022293
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9643612
X-RAY DIFFRACTIONr_angle_other_deg0.8873.0015351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66124.925134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92515423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5021512
X-RAY DIFFRACTIONr_chiral_restr0.110.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined0.2180.2528
X-RAY DIFFRACTIONr_nbd_other0.1730.22406
X-RAY DIFFRACTIONr_nbtor_refined0.190.21356
X-RAY DIFFRACTIONr_nbtor_other0.0880.21476
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1950.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0511.51599
X-RAY DIFFRACTIONr_mcbond_other0.321.5634
X-RAY DIFFRACTIONr_mcangle_it1.59222555
X-RAY DIFFRACTIONr_scbond_it2.4731167
X-RAY DIFFRACTIONr_scangle_it3.6744.51057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 95 -
Rwork0.199 3125 -
obs-3125 99.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.50050.08250.05520.75290.27220.45940.00070.03970.0033-0.0240.0213-0.0087-0.01380.0184-0.0220.0193-0.0020.00970.0240.00640.0155-10.4542-0.7620.6537
21.24170.82780.43630.92910.5440.5761-0.05250.00880.1396-0.0783-0.01750.1359-0.0941-0.07330.070.04140.015-0.01390.02920.00180.0335-25.89798.533515.7886
30.86220.04390.32380.9869-0.05781.1941-0.02270.105-0.0377-0.085-0.0056-0.0167-0.0339-0.01910.02820.0145-0.00620.01080.0316-0.00870-24.6351-6.77239.5673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 178
2X-RAY DIFFRACTION2A179 - 262
3X-RAY DIFFRACTION3A263 - 338

+
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://pdbjlvh1.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