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- PDB-6imw: The complex structure of endo-beta-1,2-glucanase mutant (E262Q) f... -

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Basic information

Entry
Database: PDB / ID: 6imw
TitleThe complex structure of endo-beta-1,2-glucanase mutant (E262Q) from Talaromyces funiculosus with beta-1,2-glucan
ComponentsEndo-beta-1,2-glucanase
KeywordsHYDROLASE / Glycoside hydrolase / Talaromyces funiculosus / sophorose / complex
Function / homologyglucan endo-1,2-beta-glucosidase / glucan endo-1,2-beta-glucosidase activity / DI(HYDROXYETHYL)ETHER / Endo-beta-1,2-glucanase
Function and homology information
Biological speciesTalaromyces funiculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Miyanaga, A. ...Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Miyanaga, A. / Yamashita, T. / Sugawara, F. / Kamakura, T. / Komba, S. / Nakai, H. / Taguchi, H.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Identification, characterization, and structural analyses of a fungal endo-beta-1,2-glucanase reveal a new glycoside hydrolase family.
Authors: Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Terada, T. / Miyanaga, A. / Yamashita, T. / Sugawara, F. ...Authors: Tanaka, N. / Nakajima, M. / Narukawa-Nara, M. / Matsunaga, H. / Kamisuki, S. / Aramasa, H. / Takahashi, Y. / Sugimoto, N. / Abe, K. / Terada, T. / Miyanaga, A. / Yamashita, T. / Sugawara, F. / Kamakura, T. / Komba, S. / Nakai, H. / Taguchi, H.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,2-glucanase
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,17214
Polymers113,2082
Non-polymers3,96412
Water4,558253
1
A: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3186
Polymers56,6041
Non-polymers1,7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint34 kcal/mol
Surface area18770 Å2
MethodPISA
2
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8548
Polymers56,6041
Non-polymers2,2507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint15 kcal/mol
Surface area17900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.169, 117.924, 93.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 24 - 517 / Label seq-ID: 12 - 505

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endo-beta-1,2-glucanase


Mass: 56603.973 Da / Num. of mol.: 2 / Mutation: E262Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Talaromyces funiculosus (fungus) / Production host: Komagataella pastoris (fungus) / Strain (production host): KM71H
References: UniProt: A0A4V8H013*PLUS, glucan endo-1,2-beta-glucosidase

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Sugars , 3 types, 10 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D- ...beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-2DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5]/1-1-1-1-1-1-1/a2-b1_b2-c1_c2-d1_d2-e1_e2-f1_f2-g1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{[(2+1)][b-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#4: 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.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

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Non-polymers , 2 types, 255 molecules

#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe authors submitted the sequence information to DDBJ and the accession number (LC430902) was assigned.

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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: 2.29 Å3/Da / Density % sol: 46.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M citrate buffer (pH 4.0), 0.1M NaCl, 25%(w/v) PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.64 Å / Num. obs: 60060 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.812 / Num. unique obs: 4375 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJune 1, 2017data reduction
Aimless0.7.3data scaling
MOLREP7.0.014phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IMU

6imu


Resolution: 2.1→46.64 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.329 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.193 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23567 3029 5 %RANDOM
Rwork0.20964 ---
obs0.21098 56981 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.348 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 260 253 8329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0148332
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177100
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.69611395
X-RAY DIFFRACTIONr_angle_other_deg0.8631.67116618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185988
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57423.753413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.555151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5061528
X-RAY DIFFRACTIONr_chiral_restr0.0550.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021638
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8091.9453955
X-RAY DIFFRACTIONr_mcbond_other0.8091.9453954
X-RAY DIFFRACTIONr_mcangle_it1.3392.9164942
X-RAY DIFFRACTIONr_mcangle_other1.3392.9164943
X-RAY DIFFRACTIONr_scbond_it1.0412.0684377
X-RAY DIFFRACTIONr_scbond_other1.042.0684377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6913.076454
X-RAY DIFFRACTIONr_long_range_B_refined2.43822.9039760
X-RAY DIFFRACTIONr_long_range_B_other2.42222.9039711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17792 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 227 -
Rwork0.311 4139 -
obs--100 %

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