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- PDB-4gzi: Active-site mutant of potato endo-1,3-beta-glucanase in complex w... -

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Basic information

Entry
Database: PDB / ID: 4gzi
TitleActive-site mutant of potato endo-1,3-beta-glucanase in complex with laminaratriose
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 / 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
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: 1.68 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.
#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 / 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_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 / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0552
Polymers36,5511
Non-polymers5041
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.895, 49.273, 57.075
Angle α, β, γ (deg.)90.00, 98.38, 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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.09 Å3/Da / Density % sol: 41.13 %
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, 0.2 mM laminarahexose, streak seeding, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8162 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Jul 2, 2006 / Details: mirrors
RadiationMonochromator: Ge(111) triangular bent crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8162 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. all: 34231 / Num. obs: 34231 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.2
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3131 / % possible all: 92.7

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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 3UR7

3ur7


Resolution: 1.68→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.947 / SU ML: 0.054 / Isotropic thermal model: Isotropic / Cross valid method: R-FREE / σ(I): -3 / ESU R: 0.085 / ESU R Free: 0.086 / Stereochemistry target values: Engh & Huber / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 1076 3.1 %RANDOM
Rwork0.1364 ---
all0.1375 33126 --
obs0.1375 33126 99.04 %-
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: 17.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-1.05 Å2
2---0.82 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.68→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2509 0 34 338 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222625
X-RAY DIFFRACTIONr_bond_other_d0.0020.022277
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9553571
X-RAY DIFFRACTIONr_angle_other_deg0.8843.0015305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2335314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2524.887133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75115422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4531512
X-RAY DIFFRACTIONr_chiral_restr0.110.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined0.2150.2506
X-RAY DIFFRACTIONr_nbd_other0.1770.22298
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21326
X-RAY DIFFRACTIONr_nbtor_other0.1020.21296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3631.52018
X-RAY DIFFRACTIONr_mcbond_other0.3031.5634
X-RAY DIFFRACTIONr_mcangle_it1.5522552
X-RAY DIFFRACTIONr_scbond_it2.76931229
X-RAY DIFFRACTIONr_scangle_it3.8854.51019
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.723 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 66 -
Rwork0.157 2219 -
obs-2219 91.55 %
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)
10.56060.00260.03450.85430.22340.52170.01490.0527-0.006-0.03780.0003-0.0327-0.00360.0017-0.0151-0.0133-0.00230.01640.00320.0043-0.0114-10.114-0.751320.4998
20.88870.65180.25750.9650.4520.6963-0.06270.02130.1042-0.10440.00010.114-0.0866-0.08810.06260.00560.0165-0.00490.0206-0.00010.0201-25.77487.878815.5883
30.947-0.07680.33371.10650.02931.3144-0.02190.108-0.0716-0.14930.0016-0.0238-0.0306-0.01220.0203-0.0041-0.00830.01160.024-0.0109-0.0268-24.0801-6.51259.1642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 178
2X-RAY DIFFRACTION2A179 - 265
3X-RAY DIFFRACTION3A266 - 338

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