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- PDB-6sxs: GH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor -

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Basic information

Entry
Database: PDB / ID: 6sxs
TitleGH54 a-l-arabinofuranosidase soaked with cyclic sulfate inhibitor
ComponentsAlpha-L-arabinofuranosidase B
KeywordsHYDROLASE / Michaelis Complex / Arabinofuranosidase / GH54 / Aspergillus
Function / homology
Function and homology information


arabinose metabolic process / arabinan catabolic process / L-arabinose metabolic process / non-reducing end alpha-L-arabinofuranosidase / alpha-L-arabinofuranosidase activity / xylan catabolic process / extracellular region
Similarity search - Function
Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B / Alpha-L-arabinofuranosidase B, catalytic / Alpha-L-arabinofuranosidase B, arabinose-binding domain / Alpha-L-arabinofuranosidase B, arabinose-binding domain superfamily / Alpha-L-arabinofuranosidase B (ABFB) domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
ACETATE ION / Chem-LX5 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alpha-L-arabinofuranosidase B
Similarity search - Component
Biological speciesAspergillus kawachii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å
AuthorsMcGregor, N.G.S. / Davies, G.J. / Nin-Hill, A. / Rovira, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R001162/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining alpha-l-Arabinofuranosidases.
Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, ...Authors: McGregor, N.G.S. / Artola, M. / Nin-Hill, A. / Linzel, D. / Haon, M. / Reijngoud, J. / Ram, A. / Rosso, M.N. / van der Marel, G.A. / Codee, J.D.C. / van Wezel, G.P. / Berrin, J.G. / Rovira, C. / Overkleeft, H.S. / Davies, G.J.
History
DepositionSep 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn
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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_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 2.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Alpha-L-arabinofuranosidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,97917
Polymers50,8841
Non-polymers2,09516
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint17 kcal/mol
Surface area16610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.136, 111.136, 342.742
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11AAA-612-

HOH

21AAA-785-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Alpha-L-arabinofuranosidase B / Arabinosidase B


Mass: 50883.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus kawachii (mold) / Gene: abfB, AKAW_08685 / Plasmid: pPICZa / Production host: Komagataella pastoris (fungus)
References: UniProt: Q8NK89, non-reducing end alpha-L-arabinofuranosidase

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Sugars , 2 types, 2 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: obtained synthetically
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: 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.: 1 / Source method: obtained synthetically / 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

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Non-polymers , 7 types, 249 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3O2
#9: Chemical ChemComp-LX5 / [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl] hydrogen sulfate


Mass: 228.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O7S / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 Å3/Da / Density % sol: 34 %
Description: Triangular prisms roughly twice as long as the triangle face is tall.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2:1 protein:well solution. 0.1 M pH 4.5 sodium acetate buffer, 60% PEG400, 0.3 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 1, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.859→84.059 Å / Num. obs: 68786 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.039 / Rrim(I) all: 0.133 / Net I/σ(I): 10.2
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 12.8 % / Rmerge(I) obs: 5.32 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 3411 / CC1/2: 0.44 / Rpim(I) all: 1.53 / Rrim(I) all: 5.54 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSMar 15, 2019data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WD3

1wd3


Resolution: 1.859→84.059 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.173 / SU B: 3.627 / SU ML: 0.095 / Average fsc free: 0.8255 / Average fsc work: 0.835 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.215 3338 4.853 %
Rwork0.1817 65448 -
all0.183 --
obs-68786 99.73 %
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: 40.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.885 Å20.443 Å2-0 Å2
2--0.885 Å2-0 Å2
3----2.872 Å2
Refinement stepCycle: LAST / Resolution: 1.859→84.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 131 235 3934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133777
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173149
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.675134
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5887336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2255480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.224.011182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75815496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5091512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02785
X-RAY DIFFRACTIONr_nbd_refined0.1960.2759
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.23192
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21885
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2269
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3110.213
X-RAY DIFFRACTIONr_nbd_other0.2160.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.28
X-RAY DIFFRACTIONr_mcbond_it3.1024.2661925
X-RAY DIFFRACTIONr_mcbond_other3.0594.2621922
X-RAY DIFFRACTIONr_mcangle_it3.6866.3842402
X-RAY DIFFRACTIONr_mcangle_other3.6886.3852403
X-RAY DIFFRACTIONr_scbond_it4.0364.5221852
X-RAY DIFFRACTIONr_scbond_other4.0354.5221853
X-RAY DIFFRACTIONr_scangle_it5.1986.6732731
X-RAY DIFFRACTIONr_scangle_other5.1976.6732732
X-RAY DIFFRACTIONr_lrange_it5.6151.6934249
X-RAY DIFFRACTIONr_lrange_other5.59151.4484206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.859-1.9070.3542390.3734677X-RAY DIFFRACTION97.5397
1.907-1.9590.3162500.3384650X-RAY DIFFRACTION99.5328
1.959-2.0160.2962250.3044570X-RAY DIFFRACTION99.9583
2.016-2.0780.282190.2644396X-RAY DIFFRACTION100
2.078-2.1460.2562140.2364328X-RAY DIFFRACTION100
2.146-2.2220.2512470.2184113X-RAY DIFFRACTION100
2.222-2.3050.232030.2044003X-RAY DIFFRACTION100
2.305-2.40.2211900.1963870X-RAY DIFFRACTION100
2.4-2.5060.1981900.1763715X-RAY DIFFRACTION100
2.506-2.6280.1991820.173552X-RAY DIFFRACTION100
2.628-2.7710.2211940.1713375X-RAY DIFFRACTION99.972
2.771-2.9390.2451590.1793197X-RAY DIFFRACTION100
2.939-3.1410.2041530.173021X-RAY DIFFRACTION99.937
3.141-3.3930.2141120.1852857X-RAY DIFFRACTION99.9663
3.393-3.7160.2111450.1832599X-RAY DIFFRACTION100
3.716-4.1540.1591320.1482349X-RAY DIFFRACTION100
4.154-4.7960.128950.1192119X-RAY DIFFRACTION100
4.796-5.8710.202730.1451816X-RAY DIFFRACTION100
5.871-8.2920.284720.1941412X-RAY DIFFRACTION100
8.292-84.0590.275440.192829X-RAY DIFFRACTION98.9796

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