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- PDB-6p2l: Crystal structure of Niastella koreensis GH74 (NkGH74) enzyme -

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Basic information

Entry
Database: PDB / ID: 6p2l
TitleCrystal structure of Niastella koreensis GH74 (NkGH74) enzyme
ComponentsGlycosyl hydrolase BNR repeat-containing protein
KeywordsHYDROLASE / glycosyl hydrolase / GH74 / xyloglucanase / 7-fold beta-propeller
Function / homologyYVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / hydrolase activity / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like fold / Mainly Beta / Glycosyl hydrolase BNR repeat-containing protein
Function and homology information
Biological speciesNiastella koreensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsStogios, P.J. / Skarina, T. / Arnal, G. / Brumer, H. / Savchenko, A.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Industrial Biocatalysis Network Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74.
Authors: Arnal, G. / Stogios, P.J. / Asohan, J. / Attia, M.A. / Skarina, T. / Viborg, A.H. / Henrissat, B. / Savchenko, A. / Brumer, H.
History
DepositionMay 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_close_contact / pdbx_validate_symm_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.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_auth_asym_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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.1Oct 11, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase BNR repeat-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,46930
Polymers73,2241
Non-polymers3,24529
Water26,1761453
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.869, 119.096, 127.043
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-1288-

HOH

21A-2174-

HOH

31A-2434-

HOH

41A-2551-

HOH

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Components

#1: Protein Glycosyl hydrolase BNR repeat-containing protein


Mass: 73224.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Niastella koreensis (strain DSM 17620 / KACC 11465 / GR20-10) (bacteria)
Strain: DSM 17620 / KACC 11465 / GR20-10 / Gene: Niako_1751 / Variant: DSM 17620 / KACC 11465 / GR20-10 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TAF2
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1225.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1a_1-5][a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-2-2-2-3-3-3-4/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1_g2-h1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1062.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5][a212h-1a_1-5]/1-1-1-1-2-2-2/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{}}}LINUCSPDB-CARE
#4: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 27
Source method: isolated from a genetically manipulated source
Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1453 / Source method: isolated from a natural source / Formula: H2O

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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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1 M ammonium sulfate, 1 M sodium chloride, 0.1 M bis-Tris propane pH 7, xyloglucan mixture

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.08→30 Å / Num. obs: 274214 / % possible obs: 98.3 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Net I/σ(I): 25.9
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 13277 / CC1/2: 0.605 / Rpim(I) all: 0.447 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.15_3448: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MGL

6mgl


Resolution: 1.08→29.128 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 13.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1397 1916 0.73 %RANDOM
Rwork0.1185 ---
obs0.1187 262890 94.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→29.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 182 1453 6704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085490
X-RAY DIFFRACTIONf_angle_d1.1127551
X-RAY DIFFRACTIONf_dihedral_angle_d14.481836
X-RAY DIFFRACTIONf_chiral_restr0.096884
X-RAY DIFFRACTIONf_plane_restr0.008957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.10560.24761300.238615989X-RAY DIFFRACTION82
1.1056-1.13550.2191050.198117076X-RAY DIFFRACTION87
1.1355-1.16890.18261390.176817475X-RAY DIFFRACTION89
1.1689-1.20670.1531300.167617693X-RAY DIFFRACTION90
1.2067-1.24980.18561410.1617928X-RAY DIFFRACTION91
1.2498-1.29980.15551310.149518296X-RAY DIFFRACTION93
1.2998-1.3590.16121240.142718640X-RAY DIFFRACTION95
1.359-1.43060.14811460.132818946X-RAY DIFFRACTION96
1.4306-1.52020.14771460.121519309X-RAY DIFFRACTION98
1.5202-1.63760.12561370.114519518X-RAY DIFFRACTION99
1.6376-1.80240.14331510.111219676X-RAY DIFFRACTION99
1.8024-2.06310.13521360.097719890X-RAY DIFFRACTION100
2.0631-2.59910.10681520.095620008X-RAY DIFFRACTION100
2.5991-29.13820.1261480.097920530X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1923-0.0114-0.01780.3290.1260.3176-0.00290.0076-0.02060.00310.0168-0.0121-0.00270.0205-0.01340.0543-0.0041-0.00710.0555-0.00460.068.888656.936837.3682
20.3060.17680.35431.07210.78931.3037-0.02820.0295-0.0002-0.1907-0.00260.0568-0.15150.0260.03250.0975-0.00240.00060.0666-0.01070.080112.891846.51644.7016
30.26530.27920.16871.1161-0.40131.71-0.03180.00330.0283-0.1057-0.04060.0973-0.0364-0.06580.06060.06330.01-0.01460.0644-0.03380.09542.9626.26491.7377
40.7261-1.2512-1.21053.14650.97353.25840.17130.3146-0.3217-0.1204-0.1426-0.32240.220.2630.00650.09240.01950.00510.1065-0.04580.212323.081922.76247.0725
50.5904-0.1152-0.29061.3080.30990.96770.00260.0013-0.05330.05370.0056-0.11820.0650.041-0.00230.05770.0011-0.01980.0576-0.02060.08816.084328.543517.428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 35:403)
2X-RAY DIFFRACTION2(chain A and resid 404:533)
3X-RAY DIFFRACTION3(chain A and resid 534:636)
4X-RAY DIFFRACTION4(chain A and resid 637:646)
5X-RAY DIFFRACTION5(chain A and resid 647:719)

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