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- PDB-6imv: The complex structure of endo-beta-1,2-glucanase from Talaromyces... -

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Basic information

Entry
Database: PDB / ID: 6imv
TitleThe complex structure of endo-beta-1,2-glucanase from Talaromyces funiculosus with sophorose
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 / beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Endo-beta-1,2-glucanase
Function and homology information
Biological speciesTalaromyces funiculosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 / pdbx_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)116,54617
Polymers113,2102
Non-polymers3,33615
Water7,134396
1
A: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4289
Polymers56,6051
Non-polymers1,8238
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint22 kcal/mol
Surface area17880 Å2
MethodPISA
2
B: Endo-beta-1,2-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1188
Polymers56,6051
Non-polymers1,5137
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint15 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.088, 118.104, 93.428
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

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: 56604.957 Da / Num. of mol.: 2
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: A0A4V8H012*PLUS, glucan endo-1,2-beta-glucosidase

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Sugars , 4 types, 12 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-glucopyranose-(1-2)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-2DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][a-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.: 7
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
#5: 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 / Feature type: SUBJECT OF INVESTIGATION
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 , 2 types, 399 molecules

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


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M phosphate-citrate buffer (pH 4.6), 0.1M NaCl, 20%(w/v) PEG3350

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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: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.71 Å / Num. obs: 69519 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.128 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.04 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.452 / Num. unique obs: 4430 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSJune 1, 2017data reduction
Aimless0.7.3data scaling
MOLREP7.0.060phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IMU

6imu


Resolution: 2→49.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.02 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.19 / ESU R Free: 0.152 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20897 3577 5.1 %RANDOM
Rwork0.18156 ---
obs0.18297 65891 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.731 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7816 0 217 396 8429
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0148301
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177097
X-RAY DIFFRACTIONr_angle_refined_deg1.1051.68711342
X-RAY DIFFRACTIONr_angle_other_deg0.8931.6716632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7995992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80423.702416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.917151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9411529
X-RAY DIFFRACTIONr_chiral_restr0.0580.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029292
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021653
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_it0.841.8553965
X-RAY DIFFRACTIONr_mcbond_other0.841.8553964
X-RAY DIFFRACTIONr_mcangle_it1.3452.7784958
X-RAY DIFFRACTIONr_mcangle_other1.3442.7784959
X-RAY DIFFRACTIONr_scbond_it1.21324336
X-RAY DIFFRACTIONr_scbond_other1.21324336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9232.9566385
X-RAY DIFFRACTIONr_long_range_B_refined2.57821.959790
X-RAY DIFFRACTIONr_long_range_B_other2.55721.9099727
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17900 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 293 -
Rwork0.255 4775 -
obs--100 %

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