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- PDB-5xbx: Crystal structure of GH45 endoglucanase EG27II in complex with ce... -

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Basic information

Entry
Database: PDB / ID: 5xbx
TitleCrystal structure of GH45 endoglucanase EG27II in complex with cellobiose
ComponentsEndo-beta-1,4-glucanase
KeywordsHYDROLASE / Cellulase / Glycoside Hydrolase Family 45
Function / homology
Function and homology information


cellulase / cellulase activity
Similarity search - Function
EXPB1-like domain 1 / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
beta-cellobiose / Endo-beta-1,4-glucanase
Similarity search - Component
Biological speciesAmpullaria crossean (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsNomura, T. / Mizutani, K. / Iwase, H. / Takahashi, N. / Mikami, B.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25450126 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean.
Authors: Nomura, T. / Iwase, H. / Saka, N. / Takahashi, N. / Mikami, B. / Mizutani, K.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _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.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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 2.1Nov 22, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,4-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6003
Polymers20,9151
Non-polymers6852
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint0 kcal/mol
Surface area7960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.472, 46.499, 92.014
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 Endo-beta-1,4-glucanase


Mass: 20915.051 Da / Num. of mol.: 1 / Fragment: UNP residues 17-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ampullaria crossean (invertebrata) / Gene: EG27II / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71 / References: UniProt: A7KMF0, cellulase
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 2
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.: 276 / 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: 1.76 Å3/Da / Density % sol: 30.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG4000, 200 mM KCl, 50 mM MES, 10 mM Cellobiose, Soaking in 255 mM Cellobiose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.8 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: May 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 71762 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 49.3
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 3335 / % possible all: 93.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WC2

1wc2


Resolution: 1.04→41.501 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.33
RfactorNum. reflection% reflection
Rfree0.1387 3508 4.9 %
Rwork0.1231 --
obs0.1239 71643 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.04→41.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 46 276 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011626
X-RAY DIFFRACTIONf_angle_d1.242243
X-RAY DIFFRACTIONf_dihedral_angle_d22.64602
X-RAY DIFFRACTIONf_chiral_restr0.105225
X-RAY DIFFRACTIONf_plane_restr0.009310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0401-1.05430.20421490.1962583X-RAY DIFFRACTION96
1.0543-1.06940.18711390.16322673X-RAY DIFFRACTION99
1.0694-1.08540.15751300.15042685X-RAY DIFFRACTION100
1.0854-1.10230.1621330.14692683X-RAY DIFFRACTION100
1.1023-1.12040.15831380.13222703X-RAY DIFFRACTION100
1.1204-1.13970.13631350.12872690X-RAY DIFFRACTION100
1.1397-1.16050.15991270.12322705X-RAY DIFFRACTION100
1.1605-1.18280.13151360.1192722X-RAY DIFFRACTION100
1.1828-1.20690.1481340.11472691X-RAY DIFFRACTION100
1.2069-1.23320.14011460.11652711X-RAY DIFFRACTION100
1.2332-1.26190.14291180.11532718X-RAY DIFFRACTION100
1.2619-1.29340.14111280.11352735X-RAY DIFFRACTION100
1.2934-1.32840.12971450.10882710X-RAY DIFFRACTION100
1.3284-1.36750.11481410.10912705X-RAY DIFFRACTION100
1.3675-1.41160.11251410.10632725X-RAY DIFFRACTION100
1.4116-1.46210.1271360.10372710X-RAY DIFFRACTION100
1.4621-1.52060.13281520.10272725X-RAY DIFFRACTION100
1.5206-1.58980.10591340.10612724X-RAY DIFFRACTION100
1.5898-1.67360.11881450.10992743X-RAY DIFFRACTION100
1.6736-1.77850.12571450.11582741X-RAY DIFFRACTION100
1.7785-1.91580.14261510.12762756X-RAY DIFFRACTION100
1.9158-2.10860.15461550.12782743X-RAY DIFFRACTION100
2.1086-2.41370.1541560.132776X-RAY DIFFRACTION100
2.4137-3.04090.16861490.13842814X-RAY DIFFRACTION100
3.0409-41.53390.11711450.11932964X-RAY DIFFRACTION100

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