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- PDB-6zpv: Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3 -

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Basic information

Entry
Database: PDB / ID: 6zpv
TitleStructure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51
Function / homologyACETATE ION
Function and homology information
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsMcGregor, N.G.S. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of a GH51 alpha-L-arabinofuranosidase from Meripilus giganteus: conserved substrate recognition from bacteria to fungi.
Authors: McGregor, N.G.S. / Turkenburg, J.P. / Morkeberg Krogh, K.B.R. / Nielsen, J.E. / Artola, M. / Stubbs, K.A. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJul 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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
AAA: MgGH51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,87920
Polymers67,6881
Non-polymers4,19219
Water19,4921082
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-59 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.953, 83.953, 256.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11AAA-801-

HOH

21AAA-1000-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein MgGH51


Mass: 67687.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Meripilus giganteus (fungus) / Production host: Aspergillus oryzae (mold) / References: non-reducing end alpha-L-arabinofuranosidase

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Sugars , 3 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: 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
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1097 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1082 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 1.8 M (NH4)2SO4, 0.1 M NaOAc, pH 5-6, 35% glycerol
PH range: 5-6

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Cooled by conduction through pin / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 1.3775 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3775 Å / Relative weight: 1
ReflectionResolution: 1.2→85.53 Å / Num. obs: 285059 / % possible obs: 100 % / Redundancy: 33 % / CC1/2: 1 / Rpim(I) all: 0.011 / Net I/σ(I): 27.2
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 25.1 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13929 / CC1/2: 0.421 / Rpim(I) all: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZPS

6zps


Resolution: 1.2→79.918 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.892 / SU ML: 0.017 / Cross valid method: FREE R-VALUE / ESU R: 0.025 / ESU R Free: 0.027
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.144 14149 4.967 %
Rwork0.1199 270712 -
all0.121 --
obs-284861 99.971 %
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: 15.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.167 Å2-0 Å2-0 Å2
2--0.167 Å2-0 Å2
3----0.334 Å2
Refinement stepCycle: LAST / Resolution: 1.2→79.918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4788 0 264 1082 6134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0135342
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174582
X-RAY DIFFRACTIONr_angle_refined_deg2.0731.6997372
X-RAY DIFFRACTIONr_angle_other_deg1.6471.60510705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96923.105248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4515713
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6561521
X-RAY DIFFRACTIONr_chiral_restr0.130.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025971
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021132
X-RAY DIFFRACTIONr_nbd_refined0.2330.21040
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.24310
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22612
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22279
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.230.2695
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3190.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.212
X-RAY DIFFRACTIONr_nbd_other0.2360.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1850.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_mcbond_it1.1591.3532573
X-RAY DIFFRACTIONr_mcbond_other1.1531.3512570
X-RAY DIFFRACTIONr_mcangle_it1.3272.0413225
X-RAY DIFFRACTIONr_mcangle_other1.3272.0413226
X-RAY DIFFRACTIONr_scbond_it4.6561.6312769
X-RAY DIFFRACTIONr_scbond_other4.6551.6322770
X-RAY DIFFRACTIONr_scangle_it4.4252.3894131
X-RAY DIFFRACTIONr_scangle_other4.4252.3894132
X-RAY DIFFRACTIONr_lrange_it3.80619.4516287
X-RAY DIFFRACTIONr_lrange_other3.68119.116232
X-RAY DIFFRACTIONr_rigid_bond_restr7.53239924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.24710630.22719716X-RAY DIFFRACTION99.9567
1.231-1.2650.22810210.20819281X-RAY DIFFRACTION99.9902
1.265-1.3020.2079580.18618806X-RAY DIFFRACTION100
1.302-1.3420.1869900.16618249X-RAY DIFFRACTION100
1.342-1.3860.1748960.14117723X-RAY DIFFRACTION100
1.386-1.4340.1559270.12217142X-RAY DIFFRACTION100
1.434-1.4880.148750.10916538X-RAY DIFFRACTION100
1.488-1.5490.1278200.0915966X-RAY DIFFRACTION99.994
1.549-1.6180.1157950.08215350X-RAY DIFFRACTION100
1.618-1.6970.1117800.07514658X-RAY DIFFRACTION100
1.697-1.7890.116910.07514029X-RAY DIFFRACTION100
1.789-1.8970.1146860.0813228X-RAY DIFFRACTION100
1.897-2.0280.1216310.09312484X-RAY DIFFRACTION99.9924
2.028-2.1910.1236570.09811620X-RAY DIFFRACTION100
2.191-2.40.1235410.09810791X-RAY DIFFRACTION100
2.4-2.6830.1334960.1099788X-RAY DIFFRACTION100
2.683-3.0980.1514440.1258690X-RAY DIFFRACTION100
3.098-3.7940.1493960.1397395X-RAY DIFFRACTION100
3.794-5.3650.1373110.1245834X-RAY DIFFRACTION100
5.365-79.9180.2261720.2073424X-RAY DIFFRACTION100

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