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- PDB-6mvj: Cellobiose complex Cel45A from Neurospora crassa OR74A -

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Basic information

Entry
Database: PDB / ID: 6mvj
TitleCellobiose complex Cel45A from Neurospora crassa OR74A
ComponentsEndoglucanase V
KeywordsHYDROLASE / Endoglucanase V Glycoside hydrolase 45 family A Cellobiose complex
Function / homology
Function and homology information


cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. ...Glycoside hydrolase, family 45 / Glycosyl hydrolase family 45 / Glycosyl hydrolases family 45 active site. / RlpA-like domain / RlpA-like domain superfamily / CBM1 (carbohydrate binding type-1) domain signature. / Cellulose-binding domain, fungal / Cellulose-binding domain superfamily / Fungal cellulose binding domain / CBM1 (carbohydrate binding type-1) domain profile. / Fungal-type cellulose-binding domain / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / Cellulase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.809 Å
AuthorsKadowaki, M.A.S. / Polikarpov, I.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Other government20111/20505-4 Brazil
CitationJournal: Biochimie / Year: 2019
Title: Structural insights into the hydrolysis pattern and molecular dynamics simulations of GH45 subfamily a endoglucanase from Neurospora crassa OR74A.
Authors: Kadowaki, M.A.S. / Polikarpov, I.
History
DepositionOct 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / 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_instance_feature / 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 / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6252
Polymers30,2821
Non-polymers3421
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint3 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.185, 72.755, 86.348
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


Mass: 30282.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus)
Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987
Gene: gh45-1, NCU05121 / Plasmid: pEXPYR / Production host: Aspergillus nidulans FGSC A4 (mold) / Variant (production host): A773 / References: UniProt: Q1K5M0
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 1.62 Å3/Da / Density % sol: 23.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM HEPES pH 8.0, 20% PEG6000 (w/w) and 10 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.809→43.17 Å / Num. obs: 18310 / % possible obs: 98.2 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rrim(I) all: 0.047 / Net I/σ(I): 40.1
Reflection shellResolution: 1.81→1.85 Å / Mean I/σ(I) obs: 14.6 / CC1/2: 0.992 / Rrim(I) all: 0.13 / % possible all: 91

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Processing

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

5glx


Resolution: 1.809→29.331 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.94
RfactorNum. reflection% reflection
Rfree0.1801 975 5.34 %
Rwork0.1462 --
obs0.148 18261 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.809→29.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1569 0 23 272 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061659
X-RAY DIFFRACTIONf_angle_d0.8742265
X-RAY DIFFRACTIONf_dihedral_angle_d2.761280
X-RAY DIFFRACTIONf_chiral_restr0.051235
X-RAY DIFFRACTIONf_plane_restr0.005301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8091-1.90450.23131310.14742353X-RAY DIFFRACTION95
1.9045-2.02380.20231250.14512385X-RAY DIFFRACTION96
2.0238-2.180.19841560.14592404X-RAY DIFFRACTION98
2.18-2.39930.19371230.14842473X-RAY DIFFRACTION97
2.3993-2.74630.21111540.15572447X-RAY DIFFRACTION99
2.7463-3.45910.16061380.15482560X-RAY DIFFRACTION100
3.4591-29.33460.14321480.13352664X-RAY DIFFRACTION100

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