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- PDB-6krn: Crystal structure of GH30 xylanase B from Talaromyces cellulolyti... -

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Basic information

Entry
Database: PDB / ID: 6krn
TitleCrystal structure of GH30 xylanase B from Talaromyces cellulolyticus expressed by Pichia pastoris in complex with aldotriuronic acid
ComponentsMating factor alpha,GH30 Xylanase B
KeywordsHYDROLASE / Xylanase / Glucuronoxylanase
Function / homology
Function and homology information


mating pheromone activity / mating / pheromone-dependent signal transduction involved in conjugation with cellular fusion / glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / extracellular region
Similarity search - Function
Mating factor alpha / Mating factor alpha, C-terminal repeat / Mating factor alpha precursor, N-terminal / Yeast mating factor alpha hormone / Mating factor alpha precursor N-terminus / Endo-beta-1,6-galactanase-like / O-Glycosyl hydrolase family 30 / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 ...Mating factor alpha / Mating factor alpha, C-terminal repeat / Mating factor alpha precursor, N-terminal / Yeast mating factor alpha hormone / Mating factor alpha precursor N-terminus / Endo-beta-1,6-galactanase-like / O-Glycosyl hydrolase family 30 / Glycosyl hydrolase family 30, beta sandwich domain / Glycosyl hydrolase family 30 beta sandwich domain / Glycoside hydrolase family 30 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
GH30 Xylanase B / Bifunctional glucuronoxylanase and xylobiohydrolase Xyn30B / Mating factor alpha
Similarity search - Component
Biological speciesSaccharomyces uvarum (yeast)
Talaromyces cellulolyticus CF-2612 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.653 Å
AuthorsNakamichi, Y. / Watanabe, M. / Inoue, H.
CitationJournal: Febs Open Bio / Year: 2020
Title: Substrate recognition by a bifunctional GH30-7 xylanase B from Talaromyces cellulolyticus.
Authors: Nakamichi, Y. / Watanabe, M. / Matsushika, A. / Inoue, H.
History
DepositionAug 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
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_validate_close_contact / 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.occupancy / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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: atom_type / chem_comp ...atom_type / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 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
A: Mating factor alpha,GH30 Xylanase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0317
Polymers59,3011
Non-polymers3,7296
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint52 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.251, 78.700, 118.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Non-polymers , 2 types, 499 molecules A

#1: Protein Mating factor alpha,GH30 Xylanase B / Alpha mating pheromone


Mass: 59301.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Mating factor alpha (UNP residues 1-89), linker, and GH30 Xylanase B (UNP residues 23-474).
Source: (gene. exp.) Saccharomyces uvarum (yeast), (gene. exp.) Talaromyces cellulolyticus CF-2612 (fungus)
Production host: Komagataella phaffii GS115 (fungus)
References: UniProt: P25501, UniProt: A0A4V8H018, UniProt: A0A510NXC4*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 4 types, 6 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.: 2
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 alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 4-O-methyl-alpha-D-glucopyranuronic acid-(1-2)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose


Type: oligosaccharide / Mass: 472.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a212h-1b_1-5][a2122A-1a_1-5_4*OC]/1-1-2/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][b-D-Xylp]{[(4+1)][b-D-Xylp]{[(2+1)][a-D-GlcpA4Me]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestY
Has protein modificationY
Sequence detailsThe sequence region is from a commercial vector pPIC9K (Thermo fisher scientific).

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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: 2.49 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: PEG 3350, HEPES, magnesium chloride

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.653→33.41 Å / Num. obs: 71087 / % possible obs: 99.41 % / Redundancy: 4.5 % / Biso Wilson estimate: 22.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04648 / Rpim(I) all: 0.02424 / Rrim(I) all: 0.05262 / Net I/σ(I): 15.35
Reflection shellResolution: 1.653→1.712 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.34 / Num. unique obs: 7017 / CC1/2: 0.847 / Rpim(I) all: 0.2389 / Rrim(I) all: 0.5184 / % possible all: 99.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XDSdata scaling
MOLREP11.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IUJ

6iuj


Resolution: 1.653→33.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.081
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1897 3554 5 %
Rwork0.1695 --
all0.171 --
obs-71087 99.496 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.318 Å2
Baniso -1Baniso -2Baniso -3
1-1.213 Å20 Å20 Å2
2--0.101 Å20 Å2
3----1.314 Å2
Refinement stepCycle: LAST / Resolution: 1.653→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 249 498 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133925
X-RAY DIFFRACTIONr_bond_other_d0.0360.0183340
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.7275346
X-RAY DIFFRACTIONr_angle_other_deg3.1791.6527811
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37823.696184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78515555
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8561514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024323
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02810
X-RAY DIFFRACTIONr_nbd_refined0.210.2679
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.23296
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22030
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1150.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2335
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.28
X-RAY DIFFRACTIONr_nbd_other0.2230.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.217
X-RAY DIFFRACTIONr_mcbond_it2.2812.3061853
X-RAY DIFFRACTIONr_mcbond_other2.2812.3041852
X-RAY DIFFRACTIONr_mcangle_it2.8923.4492325
X-RAY DIFFRACTIONr_mcangle_other2.8913.4512326
X-RAY DIFFRACTIONr_scbond_it3.2572.6042072
X-RAY DIFFRACTIONr_scbond_other3.2572.6042072
X-RAY DIFFRACTIONr_scangle_it4.2623.8073021
X-RAY DIFFRACTIONr_scangle_other4.2613.8083022
X-RAY DIFFRACTIONr_lrange_it4.87628.8374455
X-RAY DIFFRACTIONr_lrange_other4.7728.2494339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.653-1.6960.2812580.2534900X-RAY DIFFRACTION98.907
1.696-1.7420.2582540.2134819X-RAY DIFFRACTION99.9409
1.742-1.7930.2382450.2014670X-RAY DIFFRACTION99.8578
1.793-1.8480.242410.1894564X-RAY DIFFRACTION99.6268
1.848-1.9080.2022270.1744319X-RAY DIFFRACTION98.1222
1.908-1.9750.2022260.1714303X-RAY DIFFRACTION99.7138
1.975-2.0490.1882160.1674097X-RAY DIFFRACTION99.7456
2.049-2.1320.2032100.1683993X-RAY DIFFRACTION99.7626
2.132-2.2270.1672010.1633821X-RAY DIFFRACTION99.9006
2.227-2.3350.1921930.1643655X-RAY DIFFRACTION99.7925
2.335-2.460.171850.1613511X-RAY DIFFRACTION99.784
2.46-2.6090.1991730.1573290X-RAY DIFFRACTION99.6834
2.609-2.7880.1891640.1583115X-RAY DIFFRACTION99.3035
2.788-3.0090.1621530.1632913X-RAY DIFFRACTION99.7398
3.009-3.2940.1861420.172700X-RAY DIFFRACTION99.6843
3.294-3.6780.1861280.1682433X-RAY DIFFRACTION99.3406
3.678-4.2390.1751150.1432181X-RAY DIFFRACTION99.1793
4.239-5.1710.141980.1491856X-RAY DIFFRACTION99.2382
5.171-7.2270.185780.1951481X-RAY DIFFRACTION99.6166
7.227-33.410.268470.22909X-RAY DIFFRACTION99.6872

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