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- PDB-5kjq: X-ray structure of PcCel45A in complex with cellobiose expressed ... -

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Basic information

Entry
Database: PDB / ID: 5kjq
TitleX-ray structure of PcCel45A in complex with cellobiose expressed in Aspergillus nidullans
ComponentsEndoglucanase V-like protein
KeywordsSUGAR BINDING PROTEIN / endoglucanase / pccel45a / GH45 family / Phanerochaete chrysosporium / expansin / cellobiose
Function / homologyExpansin/pollen allergen, DPBB domain / Expansin, family-45 endoglucanase-like domain profile. / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta / beta-cellobiose / Endoglucanase V-like protein
Function and homology information
Biological speciesPhanerochaete chrysosporium (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.704 Å
AuthorsGodoy, A.S. / Ramia, M.P. / Camilo, C.M. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2008/56255-9, 2009/52840-7, 2009/05328-9, 2011/19100-0 and 2011/20505-4 Brazil
CitationJournal: Sci Rep / Year: 2018
Title: Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members.
Authors: Godoy, A.S. / Pereira, C.S. / Ramia, M.P. / Silveira, R.L. / Camilo, C.M. / Kadowaki, M.A. / Lange, L. / Busk, P.K. / Nascimento, A.S. / Skaf, M.S. / Polikarpov, I.
History
DepositionJun 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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

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Assembly

Deposited unit
A: Endoglucanase V-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6173
Polymers18,1791
Non-polymers4382
Water4,684260
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-14 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.271, 58.157, 62.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase V-like protein


Mass: 18178.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phanerochaete chrysosporium (fungus) / Gene: egv / Production host: Aspergillus nidulans FGSC A4 (mold) / References: UniProt: B3Y002
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellobiose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.5 M Ammonium sulfate; 0.1 M Hepes pH 7.5; 30% v/v (+/-) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Apr 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→42.7 Å / Num. obs: 34553 / % possible obs: 98 % / Redundancy: 8.4 % / Net I/σ(I): 8.4
Reflection shellHighest resolution: 1.7 Å / Redundancy: 3.49 % / Mean I/σ(I) obs: 1.8 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KJO

5kjo


Resolution: 1.704→31.454 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.85
RfactorNum. reflection% reflection
Rfree0.2045 3446 10.01 %
Rwork0.1701 --
obs0.1735 34427 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.704→31.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 28 260 1557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071348
X-RAY DIFFRACTIONf_angle_d0.8811847
X-RAY DIFFRACTIONf_dihedral_angle_d9.333759
X-RAY DIFFRACTIONf_chiral_restr0.051196
X-RAY DIFFRACTIONf_plane_restr0.005247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7037-1.72710.2628930.2294938X-RAY DIFFRACTION76
1.7271-1.75170.27591410.22631232X-RAY DIFFRACTION97
1.7517-1.77790.25531400.21851232X-RAY DIFFRACTION98
1.7779-1.80560.24351580.20171242X-RAY DIFFRACTION98
1.8056-1.83530.24131170.20071245X-RAY DIFFRACTION99
1.8353-1.86690.24851570.19411257X-RAY DIFFRACTION100
1.8669-1.90080.25121170.1881289X-RAY DIFFRACTION100
1.9008-1.93740.22491520.18251248X-RAY DIFFRACTION100
1.9374-1.97690.22081360.17931257X-RAY DIFFRACTION100
1.9769-2.01990.25841200.17511259X-RAY DIFFRACTION100
2.0199-2.06690.17971360.17411276X-RAY DIFFRACTION100
2.0669-2.11860.20281500.16811240X-RAY DIFFRACTION100
2.1186-2.17580.20791460.16551277X-RAY DIFFRACTION100
2.1758-2.23980.25871330.17341251X-RAY DIFFRACTION100
2.2398-2.31210.18591490.15981268X-RAY DIFFRACTION100
2.3121-2.39470.18141470.16731245X-RAY DIFFRACTION100
2.3947-2.49060.22261370.17111254X-RAY DIFFRACTION100
2.4906-2.60390.2571450.16871235X-RAY DIFFRACTION99
2.6039-2.74110.1811270.16811261X-RAY DIFFRACTION99
2.7411-2.91270.20551340.16231257X-RAY DIFFRACTION98
2.9127-3.13740.19481290.15621249X-RAY DIFFRACTION99
3.1374-3.45280.18631620.15061240X-RAY DIFFRACTION99
3.4528-3.95160.1621440.14231218X-RAY DIFFRACTION98
3.9516-4.97540.16111450.14611244X-RAY DIFFRACTION99
4.9754-31.45930.18861310.18451267X-RAY DIFFRACTION100

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