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- PDB-3ur7: Higher-density crystal structure of potato endo-1,3-beta-glucanase -

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Basic information

Entry
Database: PDB / ID: 3ur7
TitleHigher-density crystal structure of potato endo-1,3-beta-glucanase
ComponentsGlucan endo-1,3-beta-D-glucosidase
KeywordsHYDROLASE / glucoside hydrolase / GH17 family / pathogenesis-related class-2 protein (PR-2) / Tim Barrel / Carbohydrate/Sugar Binding
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
Glycosyl hydrolases family 17 signature. / Glycoside hydrolase family 17, plant / Glycoside hydrolase family 17 / Glycosyl hydrolases family 17 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
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: 1.4 Å
AuthorsWojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Two high-resolution structures of potato endo-1,3-beta-glucanase reveal subdomain flexibility with implications for substrate binding
Authors: Wojtkowiak, A. / Witek, K. / Hennig, J. / Jaskolski, M.
#1: Journal: Acta Biochim.Pol. / Year: 2008
Title: Conserved Cys residue influences catalytic properties of potato endo-(1-->3)-beta-glucanase GLUB20-2.
Authors: Witek, A.I. / Witek, K. / Hennig, J.
#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. / Hoj, P.B. / Fincher, G.B.
#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-Brechot, V. / Czjzek, M. / Barre, A. / Roussel, A. / Peumans, W.J. / Van Damme, E.J. / Rouge, P.
History
DepositionNov 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,2413
Polymers73,2182
Non-polymers231
Water9,116506
1
A: Glucan endo-1,3-beta-D-glucosidase


Theoretical massNumber of molelcules
Total (without water)36,6091
Polymers36,6091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucan endo-1,3-beta-D-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6322
Polymers36,6091
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.128, 49.133, 80.504
Angle α, β, γ (deg.)90.00, 102.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 36608.969 Da / Num. of mol.: 2
Fragment: mature endo-1,3-beta-glucanase, UNP residues 24-338
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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, 0.2 M ammonium acetate, 25% PEG 4000, 15 mM glucose, streak seeding, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.043 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2006 / Details: mirrors
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.043 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 110982 / Num. obs: 110982 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11024 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GHS

1ghs


Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.843 / SU ML: 0.049
Isotropic thermal model: Anisotropic model of ADP parameters
Cross valid method: R free / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS. ANISOTROPIC ADP REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1859 1117 1 %RANDOM
Rwork0.16128 ---
all0.16153 109834 --
obs0.16153 109834 99.66 %-
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: 16.815 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å20.24 Å2
2---1.38 Å20 Å2
3---2.93 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5046 0 1 506 5553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225230
X-RAY DIFFRACTIONr_bond_other_d0.0010.024567
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9297101
X-RAY DIFFRACTIONr_angle_other_deg0.935310703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63124.853272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07415864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951525
X-RAY DIFFRACTIONr_chiral_restr0.1230.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021052
X-RAY DIFFRACTIONr_nbd_refined0.2190.2986
X-RAY DIFFRACTIONr_nbd_other0.1710.24415
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22630
X-RAY DIFFRACTIONr_nbtor_other0.0850.22700
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2312
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0480.21
X-RAY DIFFRACTIONr_mcbond_it1.8971.53163
X-RAY DIFFRACTIONr_mcbond_other1.1041.51272
X-RAY DIFFRACTIONr_mcangle_it2.69125126
X-RAY DIFFRACTIONr_scbond_it3.62532123
X-RAY DIFFRACTIONr_scangle_it5.1364.51975
X-RAY DIFFRACTIONr_rigid_bond_restr1.706310151
X-RAY DIFFRACTIONr_sphericity_free10.3573507
X-RAY DIFFRACTIONr_sphericity_bonded6.28639667
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 96 -
Rwork0.225 7675 -
obs-7675 95.64 %

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