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- PDB-5m60: Chaetomium thermophilum beta-1-3-glucanase -

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Basic information

Entry
Database: PDB / ID: 5m60
TitleChaetomium thermophilum beta-1-3-glucanase
ComponentsBeta-1,3-glucanase
KeywordsTRANSFERASE / cellulose / glucanase / fungus / thermostability / glucans
Function / homology
Function and homology information


polygalacturonase activity
Similarity search - Function
Polygalacturonase QRT3-like / Pectate lyase superfamily protein / Pectate lyase superfamily protein / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / Beta-1,3-glucanase / Exo-beta-1,3-glucanase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsPapageorgiou, A.C. / Chen, J. / Li, D.
Citation
Journal: Biochim. Biophys. Acta / Year: 2017
Title: Crystal structure and biological implications of a glycoside hydrolase family 55 beta-1,3-glucanase from Chaetomium thermophilum.
Authors: Papageorgiou, A.C. / Chen, J. / Li, D.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Expression, purification and crystallization of a family 55 beta-1,3-glucanase from Chaetomium thermophilum.
Authors: Papageorgiou, A.C. / Li, D.
History
DepositionOct 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Mar 11, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Polymer sequence
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / pdbx_nonpoly_scheme / pdbx_validate_close_contact
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 / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_validate_close_contact.auth_seq_id_2
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / pdbx_struct_conn_angle / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2055
Polymers82,1531
Non-polymers1,0524
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint7 kcal/mol
Surface area23210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.661, 83.535, 65.171
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-1,3-glucanase


Mass: 82152.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Pyroglutamic acid as first residue in the structure owing to post-translational modification of glutamine at the N-terminal
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: gluN / Production host: Komagataella pastoris (fungus) / References: UniProt: D8UU87, UniProt: G0S3N2*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 694 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.6 % / Description: Rods
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 1.8 M Na/K phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→44.3 Å / Num. obs: 106298 / % possible obs: 99.8 % / Redundancy: 4.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.009 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.582 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→44.291 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.91
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 5337 5.02 %Random
Rwork0.157 ---
obs0.1582 106263 97.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 69 694 6540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066137
X-RAY DIFFRACTIONf_angle_d0.8658424
X-RAY DIFFRACTIONf_dihedral_angle_d12.1983615
X-RAY DIFFRACTIONf_chiral_restr0.059931
X-RAY DIFFRACTIONf_plane_restr0.0061124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51710.29351800.27153337X-RAY DIFFRACTION96
1.5171-1.53490.29941520.26383279X-RAY DIFFRACTION97
1.5349-1.55360.27361810.24793316X-RAY DIFFRACTION96
1.5536-1.57330.27041540.24073305X-RAY DIFFRACTION97
1.5733-1.5940.26431710.22983314X-RAY DIFFRACTION96
1.594-1.61580.24761610.22773349X-RAY DIFFRACTION97
1.6158-1.63890.25311800.22213315X-RAY DIFFRACTION96
1.6389-1.66340.27221690.22223318X-RAY DIFFRACTION97
1.6634-1.68940.23681810.22173276X-RAY DIFFRACTION96
1.6894-1.71710.25571570.19773383X-RAY DIFFRACTION97
1.7171-1.74670.22331900.19713296X-RAY DIFFRACTION98
1.7467-1.77840.22371910.19313325X-RAY DIFFRACTION97
1.7784-1.81270.2151920.17933386X-RAY DIFFRACTION97
1.8127-1.84970.20761750.17223343X-RAY DIFFRACTION98
1.8497-1.88990.2061900.16673312X-RAY DIFFRACTION97
1.8899-1.93380.18091690.16323371X-RAY DIFFRACTION97
1.9338-1.98220.19581650.15713375X-RAY DIFFRACTION98
1.9822-2.03580.16591870.15163382X-RAY DIFFRACTION98
2.0358-2.09570.18111830.1493328X-RAY DIFFRACTION98
2.0957-2.16330.1531910.14053374X-RAY DIFFRACTION98
2.1633-2.24070.16531840.13923373X-RAY DIFFRACTION98
2.2407-2.33040.18441530.14313448X-RAY DIFFRACTION99
2.3304-2.43640.1791700.1463383X-RAY DIFFRACTION99
2.4364-2.56480.1821780.14763398X-RAY DIFFRACTION98
2.5648-2.72550.16731970.14473400X-RAY DIFFRACTION99
2.7255-2.93590.15521850.14283423X-RAY DIFFRACTION99
2.9359-3.23130.17161930.13823427X-RAY DIFFRACTION99
3.2313-3.69870.14621910.12193435X-RAY DIFFRACTION99
3.6987-4.65910.12431850.11113450X-RAY DIFFRACTION99
4.6591-44.31070.17041820.16113505X-RAY DIFFRACTION99

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