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- PDB-5ofl: Crystal structure of CbXyn10C variant E140Q/E248Q complexed with ... -

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Basic information

Entry
Database: PDB / ID: 5ofl
TitleCrystal structure of CbXyn10C variant E140Q/E248Q complexed with cellohexaose
ComponentsGlycoside hydrolase family 48
KeywordsHYDROLASE / xylanase / GH10 family / cellulase
Function / homology
Function and homology information


cellulose binding / cellulase activity / cellulose catabolic process / membrane
Similarity search - Function
Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycosyl hydrolases family 10, active site ...Endoglucanase F, domain 2 / Endoglucanase F, domain 3 / Glycoside hydrolase, 48F / Glycosyl hydrolase family 48 / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / CBM2/CBM3, carbohydrate-binding domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-cellohexaose / Glycoside hydrolase family 48
Similarity search - Component
Biological speciesCaldicellulosiruptor bescii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.871 Å
AuthorsHakulinen, N. / Penttinen, L. / Rouvinen, J.
Funding support Finland, 2items
OrganizationGrant numberCountry
Academy of Finland256937 Finland
Academy of Finland292705 Finland
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose.
Authors: Chu, Y. / Tu, T. / Penttinen, L. / Xue, X. / Wang, X. / Yi, Z. / Gong, L. / Rouvinen, J. / Luo, H. / Hakulinen, N. / Yao, B. / Su, X.
History
DepositionJul 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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_struct_special_symmetry / pdbx_validate_symm_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_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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycoside hydrolase family 48
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,19710
Polymers39,3711
Non-polymers1,8269
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-64 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.830, 185.830, 56.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-790-

HOH

21A-804-

HOH

31A-810-

HOH

41A-829-

HOH

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Components

#1: Protein Glycoside hydrolase family 48


Mass: 39371.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria)
Gene: Athe_1857 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKT7
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellohexaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellohexaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 4% PEG20000, 0.2 M ammonium sulphate, 0.1 M sodium cacodalate at pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.871→131.402 Å / Num. obs: 40841 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.998 / Rrim(I) all: 0.117 / Net I/σ(I): 11.5
Reflection shellResolution: 1.871→1.903 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2006 / CC1/2: 0.759 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OFJ

5ofj


Resolution: 1.871→131.402 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 2042 5 %
Rwork0.1519 --
obs0.1534 40826 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.871→131.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 116 333 3229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013042
X-RAY DIFFRACTIONf_angle_d1.1524152
X-RAY DIFFRACTIONf_dihedral_angle_d10.7761754
X-RAY DIFFRACTIONf_chiral_restr0.06443
X-RAY DIFFRACTIONf_plane_restr0.007515

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