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- PDB-5xc9: Crystal structure of GH45 endoglucanase EG27II at pH8.0, in compl... -

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Basic information

Entry
Database: PDB / ID: 5xc9
TitleCrystal structure of GH45 endoglucanase EG27II at pH8.0, 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: 1.28 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 22, 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 2.2Oct 9, 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
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-0 kcal/mol
Surface area8000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.021, 47.278, 92.695
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.: 158 / 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: 1.83 Å3/Da / Density % sol: 32.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG4000, 200 mM KCl, 50 mM MES, 10 mM Cellobiose

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→50 Å / Num. obs: 40517 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 44
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1979 / % possible all: 99.7

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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: 1.28→42.116 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 10.03
RfactorNum. reflection% reflection
Rfree0.1323 1990 4.92 %
Rwork0.1053 --
obs0.1066 40449 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.28→42.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 46 158 1564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011616
X-RAY DIFFRACTIONf_angle_d1.2532235
X-RAY DIFFRACTIONf_dihedral_angle_d20.479629
X-RAY DIFFRACTIONf_chiral_restr0.099226
X-RAY DIFFRACTIONf_plane_restr0.009310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2799-1.31190.16661240.12022654X-RAY DIFFRACTION98
1.3119-1.34740.1551460.1092724X-RAY DIFFRACTION100
1.3474-1.3870.1181560.09922682X-RAY DIFFRACTION100
1.387-1.43180.131470.09032702X-RAY DIFFRACTION100
1.4318-1.4830.11621470.08382710X-RAY DIFFRACTION100
1.483-1.54240.11521210.08132738X-RAY DIFFRACTION100
1.5424-1.61260.11181430.07922710X-RAY DIFFRACTION100
1.6126-1.69760.11291420.08452736X-RAY DIFFRACTION100
1.6976-1.80390.13391550.08892733X-RAY DIFFRACTION100
1.8039-1.94320.11051320.09312758X-RAY DIFFRACTION100
1.9432-2.13880.11991570.09942741X-RAY DIFFRACTION100
2.1388-2.44820.15021500.11692775X-RAY DIFFRACTION100
2.4482-3.08440.13681300.13142832X-RAY DIFFRACTION100
3.0844-42.13910.14311400.11092964X-RAY DIFFRACTION100

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