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- PDB-5xc2: Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomu... -

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Basic information

Entry
Database: PDB / ID: 5xc2
TitleCrystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose
ComponentsEndo-beta-1,3-glucanase
KeywordsHYDROLASE / glycoside hydrolase family 81 / catalytic mechanism
Function / homology
Function and homology information


: / endo-1,3(4)-beta-glucanase activity / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / extracellular region
Similarity search - Function
glycoside hydrolase family 81 endo-[beta] glucanase / Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Golgi alpha-mannosidase II; domain 4 / Immunoglobulin FC, subunit C / Beta-galactosidase; Chain A, domain 5 ...glycoside hydrolase family 81 endo-[beta] glucanase / Glycosyl hydrolase family 81, N-terminal / Glycosyl hydrolase family 81 N-terminal domain / Endo-1,3(4)-beta-glucanase / Glycosyl hydrolase family 81, C-terminal domain / Glycosyl hydrolase family 81 C-terminal domain / Glycosyl hydrolases family 81 (GH81) domain profile. / Golgi alpha-mannosidase II; domain 4 / Immunoglobulin FC, subunit C / Beta-galactosidase; Chain A, domain 5 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Distorted Sandwich / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
beta-laminaribiose / Glucan endo-1,3-beta-D-glucosidase 1
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsQin, Z. / Yang, S. / Peng, Z. / Yan, Q. / Jiang, Z.
CitationJournal: To Be Published
Title: Catalytic mechanism of glycoside hydrolase family 81 beta-1,3-glucanase
Authors: Yang, S. / Qin, Z. / Zhou, P. / Yan, Q. / Jiang, Z.
History
DepositionMar 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Nov 22, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / 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_initial_refinement_model / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endo-beta-1,3-glucanase
B: Endo-beta-1,3-glucanase
C: Endo-beta-1,3-glucanase
D: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,02818
Polymers358,3444
Non-polymers8,68414
Water8,629479
1
A: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,0724
Polymers89,5861
Non-polymers2,4863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9466
Polymers89,5861
Non-polymers2,3605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5864
Polymers89,5861
Non-polymers2,0003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endo-beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4244
Polymers89,5861
Non-polymers1,8383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.700, 99.020, 138.430
Angle α, β, γ (deg.)90.00, 111.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Non-polymers , 2 types, 483 molecules ABCD

#1: Protein
Endo-beta-1,3-glucanase


Mass: 89586.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizomucor miehei (fungus)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A023I7E1, glucan endo-1,3-beta-D-glucosidase
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 14 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][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-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a3-b1_b3-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide
beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
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
[][D-1-deoxy-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose / beta-laminaribiose


Type: oligosaccharide, Oligosaccharide / Class: Antimicrobial / Mass: 342.297 Da / Num. of mol.: 2
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
[][D-1-deoxy-Glcp]{[(3+1)][b-D-Glcp]{}}LINUCSPDB-CARE

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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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: laminarihexaose (G6) was added to the protein solution at a final concentration of 1%(w/v). The complex crystals were obtained in a reservoir solution containing 24%(w/v) PEG4000, 80 mM Tris- ...Details: laminarihexaose (G6) was added to the protein solution at a final concentration of 1%(w/v). The complex crystals were obtained in a reservoir solution containing 24%(w/v) PEG4000, 80 mM Tris-HCl (pH 8.5), and 6%(v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 74950 / % possible obs: 99.55 % / Redundancy: 17 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.37
Reflection shellResolution: 2.7→2.94 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.36 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4k3a

4k3a


Resolution: 2.7→29.73 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 2005 2.68 %
Rwork0.1762 --
obs0.1777 74932 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22004 0 583 479 23066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923580
X-RAY DIFFRACTIONf_angle_d1.39432148
X-RAY DIFFRACTIONf_dihedral_angle_d13.7388262
X-RAY DIFFRACTIONf_chiral_restr0.0923638
X-RAY DIFFRACTIONf_plane_restr0.0074054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.28961410.21885177X-RAY DIFFRACTION99
2.7675-2.84220.36041470.23555161X-RAY DIFFRACTION99
2.8422-2.92580.31451390.2335167X-RAY DIFFRACTION99
2.9258-3.02020.30441400.24235196X-RAY DIFFRACTION100
3.0202-3.1280.31191420.21535139X-RAY DIFFRACTION99
3.128-3.25310.25541490.2025201X-RAY DIFFRACTION100
3.2531-3.40090.25241430.20015229X-RAY DIFFRACTION100
3.4009-3.580.2461380.18085177X-RAY DIFFRACTION100
3.58-3.80380.22351410.16815212X-RAY DIFFRACTION100
3.8038-4.09680.20521440.15785225X-RAY DIFFRACTION100
4.0968-4.50780.19271430.14195227X-RAY DIFFRACTION100
4.5078-5.15720.18851470.13975216X-RAY DIFFRACTION99
5.1572-6.48640.20271420.16795251X-RAY DIFFRACTION100
6.4864-29.73130.20891490.16375349X-RAY DIFFRACTION100

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