[English] 日本語
Yorodumi
- PDB-6yp1: HiCel7B unliganded -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yp1
TitleHiCel7B unliganded
ComponentsEndoglucanase 1Cellulase
KeywordsHYDROLASE / cellulase / glycosidase / 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 / Endoglucanase 1
Similarity search - Component
Biological speciesHumicola insolens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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 2.0Oct 13, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / diffrn_source / entity / pdbx_database_proc / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_seq_map_depositor_info / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.pdbx_auth_asym_id / _atom_site.pdbx_auth_atom_name / _atom_site.pdbx_auth_comp_id / _atom_site.pdbx_auth_seq_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_PDB_atom_name / _atom_site_anisotrop.pdbx_PDB_residue_name / _atom_site_anisotrop.pdbx_PDB_residue_no / _atom_site_anisotrop.pdbx_PDB_strand_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_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _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_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands
Revision 2.1Jan 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Endoglucanase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,43718
Polymers44,6101
Non-polymers1,82717
Water7,044391
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-66 kcal/mol
Surface area16860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.310, 92.310, 100.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11AAA-706-

ACM

21AAA-706-

ACM

-
Components

-
Protein / Sugars , 2 types, 3 molecules AAA

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


Mass: 44610.145 Da / Num. of mol.: 1
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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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

-
Non-polymers , 4 types, 406 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


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


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12 mg/mL protein in 20 mM pH 8 Tris-HCl mixed 2:1 with 0.15 M sodium citrate, 0.8 M ammonium sulfate, 1 M lithium sulfate

-
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: 1.2→46.198 Å / Num. obs: 135228 / % possible obs: 99.8 % / Redundancy: 14 % / Rrim(I) all: 0.053 / Net I/σ(I): 26.7
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 9151 / Rrim(I) all: 0.483 / % possible all: 96.3

-
Processing

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

2a39


Resolution: 1.2→46.198 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.137 / WRfactor Rwork: 0.118 / SU B: 0.684 / SU ML: 0.014 / Average fsc free: 0.9788 / Average fsc work: 0.9823 / Cross valid method: FREE R-VALUE / ESU R: 0.028 / ESU R Free: 0.028
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1353 6795 5.025 %
Rwork0.1167 128433 -
all0.118 --
obs-135228 99.683 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.352 Å20 Å2-0 Å2
2--0.352 Å2-0 Å2
3----0.704 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 115 391 3579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0133344
X-RAY DIFFRACTIONr_bond_other_d0.0060.0172879
X-RAY DIFFRACTIONr_angle_refined_deg2.321.6644551
X-RAY DIFFRACTIONr_angle_other_deg1.7181.5866743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7635419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36723.193166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71515517
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4441515
X-RAY DIFFRACTIONr_chiral_restr0.1310.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023734
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02678
X-RAY DIFFRACTIONr_nbd_refined0.2570.2629
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.22726
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21606
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.21512
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1360.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.215
X-RAY DIFFRACTIONr_nbd_other0.230.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.229
X-RAY DIFFRACTIONr_mcbond_it1.181.0931625
X-RAY DIFFRACTIONr_mcbond_other1.181.0941626
X-RAY DIFFRACTIONr_mcangle_it1.4851.6522034
X-RAY DIFFRACTIONr_mcangle_other1.4851.6532035
X-RAY DIFFRACTIONr_scbond_it4.9891.4571719
X-RAY DIFFRACTIONr_scbond_other4.991.4571718
X-RAY DIFFRACTIONr_scangle_it4.6052.0692507
X-RAY DIFFRACTIONr_scangle_other4.6042.0692508
X-RAY DIFFRACTIONr_lrange_it3.81814.6453745
X-RAY DIFFRACTIONr_lrange_other3.63214.1083658
X-RAY DIFFRACTIONr_rigid_bond_restr8.18636223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2485020.2199151X-RAY DIFFRACTION97.0639
1.231-1.2650.1675060.1549105X-RAY DIFFRACTION99.7923
1.265-1.3020.1544760.1228914X-RAY DIFFRACTION99.883
1.302-1.3420.1374320.18706X-RAY DIFFRACTION99.9562
1.342-1.3860.1144420.0848415X-RAY DIFFRACTION99.9323
1.386-1.4340.1094300.088119X-RAY DIFFRACTION99.9299
1.434-1.4880.1074090.0817901X-RAY DIFFRACTION99.9399
1.488-1.5490.1073660.0817599X-RAY DIFFRACTION99.8997
1.549-1.6180.1084060.0847281X-RAY DIFFRACTION100
1.618-1.6970.1033960.0876943X-RAY DIFFRACTION99.9591
1.697-1.7890.1163480.0896641X-RAY DIFFRACTION99.9428
1.789-1.8970.1093630.0926295X-RAY DIFFRACTION99.94
1.897-2.0280.1193340.0995877X-RAY DIFFRACTION99.9356
2.028-2.1910.1142700.1045579X-RAY DIFFRACTION99.9658
2.191-2.3990.1182570.1085137X-RAY DIFFRACTION99.9815
2.399-2.6820.152460.1194648X-RAY DIFFRACTION99.9387
2.682-3.0970.1561920.1364166X-RAY DIFFRACTION99.9771
3.097-3.7920.1471900.1363520X-RAY DIFFRACTION99.9461
3.792-5.3590.1521450.1392792X-RAY DIFFRACTION99.898
5.359-46.1980.235850.2321644X-RAY DIFFRACTION99.5394

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more