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- PDB-6yoz: HiCel7B labelled with b-1,4-glucosyl cyclophellitol -

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Basic information

Entry
Database: PDB / ID: 6yoz
TitleHiCel7B labelled with b-1,4-glucosyl cyclophellitol
ComponentsEndoglucanase 1
KeywordsHYDROLASE / cellulase / glycosidase / cyclophellitol / GH7
Function / homology
Function and homology information


cellulase / cellulase activity / cellulose catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase, family 7 / Glycoside hydrolase family 7, catalytic domain superfamily / Glycosyl hydrolase family 7 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETAMIDE / beta-D-glucopyranose / Chem-YLL / Endoglucanase 1
Similarity search - Component
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMcGregor, N.G.S. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
CitationJournal: Rsc Chem Biol / Year: 2020
Title: Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases.
Authors: de Boer, C. / McGregor, N.G.S. / Peterse, E. / Schroder, S.P. / Florea, B.I. / Jiang, J. / Reijngoud, J. / Ram, A.F.J. / van Wezel, G.P. / van der Marel, G.A. / Codee, J.D.C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._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_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code
Revision 1.2Oct 13, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_data_processing_status ...entity_src_gen / pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.gene_src_common_name / _pdbx_seq_map_depositor_info.one_letter_code ..._entity_src_gen.gene_src_common_name / _pdbx_seq_map_depositor_info.one_letter_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 1.3Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Endoglucanase 1
BBB: Endoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,85926
Polymers88,7382
Non-polymers3,12224
Water9,350519
1
AAA: Endoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,90913
Polymers44,3691
Non-polymers1,54012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Endoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,95013
Polymers44,3691
Non-polymers1,58112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.000, 102.000, 278.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11AAA-511-

ACM

21BBB-790-

HOH

31BBB-846-

HOH

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Endoglucanase 1 / Cellulase 1 / Endo-1 / 4-beta-glucanase 1 / Endoglucanase I


Mass: 44368.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Gene: CEL7B / Production host: Aspergillus oryzae (mold) / References: UniProt: P56680, cellulase

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Sugars , 2 types, 6 molecules

#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 537 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ACM / ACETAMIDE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 4.1 Å3/Da / Density % sol: 69.99 % / Description: tetragonal bipyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12 mg/mL protein in 20 mM pH 8 Tris buffer mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.88→57.621 Å / Num. obs: 120246 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 1 / Rrim(I) all: 0.177 / Net I/σ(I): 14.2
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 16.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8348 / CC1/2: 0.5 / Rrim(I) all: 2.978 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A39

2a39


Resolution: 1.88→57.621 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: FREE R-VALUE / ESU R: 0.108 / ESU R Free: 0.11
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 5995 4.986 %Random selection
Rwork0.2018 ---
all0.203 ---
obs-120246 99.947 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.655 Å2-0 Å2-0 Å2
2--0.655 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.88→57.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6100 0 184 519 6803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136467
X-RAY DIFFRACTIONr_bond_other_d0.0360.0175543
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6698799
X-RAY DIFFRACTIONr_angle_other_deg2.4571.58812942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.375800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.78222.825315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.39215964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7021530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027250
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021334
X-RAY DIFFRACTIONr_nbd_refined0.2260.21260
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.25266
X-RAY DIFFRACTIONr_nbtor_refined0.170.23084
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2433
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.6440.217
X-RAY DIFFRACTIONr_nbd_other0.2620.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1910.214
X-RAY DIFFRACTIONr_mcbond_it3.0893.4333194
X-RAY DIFFRACTIONr_mcbond_other3.0813.4323193
X-RAY DIFFRACTIONr_mcangle_it3.8875.1373990
X-RAY DIFFRACTIONr_mcangle_other3.8915.1373991
X-RAY DIFFRACTIONr_scbond_it3.9383.7433271
X-RAY DIFFRACTIONr_scbond_other3.9383.7423268
X-RAY DIFFRACTIONr_scangle_it5.5165.4934804
X-RAY DIFFRACTIONr_scangle_other5.5175.4924799
X-RAY DIFFRACTIONr_lrange_it6.46441.2277191
X-RAY DIFFRACTIONr_lrange_other6.40340.8637086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9290.4074330.3658348X-RAY DIFFRACTION99.8635
1.929-1.9820.3554000.3518122X-RAY DIFFRACTION100
1.982-2.0390.3434360.3267906X-RAY DIFFRACTION100
2.039-2.1020.3594000.3157653X-RAY DIFFRACTION99.9876
2.102-2.1710.3194040.3027473X-RAY DIFFRACTION99.9619
2.171-2.2470.3323560.2917198X-RAY DIFFRACTION99.9603
2.247-2.3320.33690.2516999X-RAY DIFFRACTION100
2.332-2.4270.2743380.2316732X-RAY DIFFRACTION100
2.427-2.5350.2493770.2116435X-RAY DIFFRACTION100
2.535-2.6590.2343320.1966161X-RAY DIFFRACTION100
2.659-2.8020.243260.2015877X-RAY DIFFRACTION100
2.802-2.9720.2352710.195613X-RAY DIFFRACTION100
2.972-3.1780.2352820.1925263X-RAY DIFFRACTION100
3.178-3.4320.2292540.1844942X-RAY DIFFRACTION100
3.432-3.760.2022470.1684539X-RAY DIFFRACTION100
3.76-4.2030.1672230.1434128X-RAY DIFFRACTION100
4.203-4.8530.1611830.1283724X-RAY DIFFRACTION100
4.853-5.9440.2211590.1823148X-RAY DIFFRACTION100
5.944-8.4040.2011280.2032507X-RAY DIFFRACTION100
8.404-57.6210.235770.2061484X-RAY DIFFRACTION99.4268

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