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- PDB-5m5z: Chaetomium thermophilum beta-1-3-glucanase -

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Basic information

Entry
Database: PDB / ID: 5m5z
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-1,3-glucanase / Exo-beta-1,3-glucanase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Polymer sequence
Category: atom_site / chem_comp ...atom_site / chem_comp / entity_poly / pdbx_nonpoly_scheme / 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 / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site_gen.auth_seq_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 3.1Jan 17, 2024Group: 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: Beta-1,3-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5958
Polymers82,1531
Non-polymers1,4427
Water21,2041177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint2 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.774, 85.277, 66.765
Angle α, β, γ (deg.)90.00, 92.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-1,3-glucanase


Mass: 82152.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The mature protein starts from a Gln residue which was found post-translationally modified to pyroglutamate (PCA)
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: gluN / Production host: Komagataella pastoris CBS 7435 (fungus) / References: UniProt: D8UU87, UniProt: G0S3N2*PLUS

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Sugars , 2 types, 4 molecules

#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: obtained synthetically
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-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 1180 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1177 / 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: 2.19 Å3/Da / Density % sol: 43.91 % / 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: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.25→45 Å / Num. obs: 424202 / % possible obs: 92.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 6.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.4
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 4.6 / CC1/2: 0.94 / % possible all: 65.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3eqn

3eqn


Resolution: 1.25→35.923 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.47
RfactorNum. reflection% reflectionSelection details
Rfree0.1405 9182 5.04 %Random
Rwork0.1226 ---
obs0.1235 182131 92.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.25→35.923 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5777 0 92 1177 7046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056156
X-RAY DIFFRACTIONf_angle_d0.8838443
X-RAY DIFFRACTIONf_dihedral_angle_d14.4652228
X-RAY DIFFRACTIONf_chiral_restr0.084933
X-RAY DIFFRACTIONf_plane_restr0.0061125
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.26420.15252280.13073987X-RAY DIFFRACTION65
1.2642-1.27910.16992270.13074340X-RAY DIFFRACTION70
1.2791-1.29470.15682370.12914839X-RAY DIFFRACTION78
1.2947-1.31110.1732750.13135411X-RAY DIFFRACTION86
1.3111-1.32830.17162770.12065734X-RAY DIFFRACTION92
1.3283-1.34650.14633170.11785843X-RAY DIFFRACTION94
1.3465-1.36580.16663350.11715876X-RAY DIFFRACTION95
1.3658-1.38610.14142890.11175853X-RAY DIFFRACTION94
1.3861-1.40780.1392550.10985947X-RAY DIFFRACTION95
1.4078-1.43090.14642930.11035855X-RAY DIFFRACTION95
1.4309-1.45560.14353120.1095816X-RAY DIFFRACTION93
1.4556-1.4820.15292810.10935884X-RAY DIFFRACTION93
1.482-1.51050.13612950.10425930X-RAY DIFFRACTION96
1.5105-1.54140.14872970.1035994X-RAY DIFFRACTION96
1.5414-1.57490.12243040.10316006X-RAY DIFFRACTION96
1.5749-1.61150.13623260.10215951X-RAY DIFFRACTION96
1.6115-1.65180.11872930.11035964X-RAY DIFFRACTION96
1.6518-1.69650.13853480.11625891X-RAY DIFFRACTION95
1.6965-1.74640.14493200.11825829X-RAY DIFFRACTION94
1.7464-1.80280.14943200.12135982X-RAY DIFFRACTION96
1.8028-1.86720.15343300.12535944X-RAY DIFFRACTION96
1.8672-1.9420.14033330.12365970X-RAY DIFFRACTION96
1.942-2.03030.1353720.11715994X-RAY DIFFRACTION97
2.0303-2.13740.13773210.11875961X-RAY DIFFRACTION96
2.1374-2.27120.143530.12125890X-RAY DIFFRACTION95
2.2712-2.44660.15623220.1286083X-RAY DIFFRACTION98
2.4466-2.69270.14113530.13346006X-RAY DIFFRACTION97
2.6927-3.08220.13262920.13936025X-RAY DIFFRACTION96
3.0822-3.88250.1283360.12876075X-RAY DIFFRACTION97
3.8825-35.93750.13453410.13116038X-RAY DIFFRACTION95

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