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- PDB-6zpx: Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 1 -

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Basic information

Entry
Database: PDB / ID: 6zpx
TitleStructure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 1
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)69,5836
Polymers67,6881
Non-polymers1,8955
Water11,584643
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint18 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.980, 65.801, 193.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#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.: 3
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-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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→82.28 Å / Num. obs: 188207 / % possible obs: 100 % / Redundancy: 7.8 % / CC1/2: 0.998 / Rpim(I) all: 0.035 / Net I/σ(I): 6.9
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 6 % / Num. unique obs: 9226 / CC1/2: 0.778 / Rpim(I) all: 0.422 / % possible all: 99.7

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Processing

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

6zps


Resolution: 1.3→62.362 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.155 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2174 9384 4.99 %
Rwork0.1781 178687 -
all0.18 --
obs-188071 99.86 %
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: 18.808 Å2
Baniso -1Baniso -2Baniso -3
1-3.335 Å2-0 Å20 Å2
2---1.622 Å2-0 Å2
3----1.713 Å2
Refinement stepCycle: LAST / Resolution: 1.3→62.362 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 124 643 5536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0135114
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174421
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.6797042
X-RAY DIFFRACTIONr_angle_other_deg1.5931.58910295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3655650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44223.291237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7591518
X-RAY DIFFRACTIONr_chiral_restr0.1180.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025840
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021107
X-RAY DIFFRACTIONr_nbd_refined0.2020.2948
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24127
X-RAY DIFFRACTIONr_nbtor_refined0.180.22514
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22229
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2434
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0950.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0490.21
X-RAY DIFFRACTIONr_nbd_other0.1140.217
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.216
X-RAY DIFFRACTIONr_mcbond_it1.8341.8532543
X-RAY DIFFRACTIONr_mcbond_other1.8181.8522542
X-RAY DIFFRACTIONr_mcangle_it2.0772.7893188
X-RAY DIFFRACTIONr_mcangle_other2.0842.7893189
X-RAY DIFFRACTIONr_scbond_it2.6222.0622571
X-RAY DIFFRACTIONr_scbond_other2.6222.0622571
X-RAY DIFFRACTIONr_scangle_it2.7973.0293846
X-RAY DIFFRACTIONr_scangle_other2.8013.033847
X-RAY DIFFRACTIONr_lrange_it2.67323.3385783
X-RAY DIFFRACTIONr_lrange_other2.55222.8285646
X-RAY DIFFRACTIONr_rigid_bond_restr3.84339535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.3340.3336290.3413150X-RAY DIFFRACTION99.588
1.334-1.370.3287190.31212725X-RAY DIFFRACTION99.9182
1.37-1.410.3156250.29112376X-RAY DIFFRACTION99.8387
1.41-1.4530.36090.27312090X-RAY DIFFRACTION99.7878
1.453-1.5010.2816450.24811672X-RAY DIFFRACTION99.8379
1.501-1.5540.2546070.21911275X-RAY DIFFRACTION99.8991
1.554-1.6120.2125090.19511041X-RAY DIFFRACTION99.9135
1.612-1.6780.1995540.17110531X-RAY DIFFRACTION99.9459
1.678-1.7530.2195270.15510124X-RAY DIFFRACTION99.9156
1.753-1.8380.2075140.1449687X-RAY DIFFRACTION99.9902
1.838-1.9380.1985440.1489188X-RAY DIFFRACTION99.9692
1.938-2.0550.1994570.1538723X-RAY DIFFRACTION99.9891
2.055-2.1970.1964340.1458253X-RAY DIFFRACTION99.931
2.197-2.3730.2054170.1397658X-RAY DIFFRACTION99.9629
2.373-2.5990.1814000.147068X-RAY DIFFRACTION99.9866
2.599-2.9060.2063300.1496452X-RAY DIFFRACTION99.9705
2.906-3.3560.2172840.1795749X-RAY DIFFRACTION100
3.356-4.1090.2132500.194880X-RAY DIFFRACTION100
4.109-5.810.1952100.1573823X-RAY DIFFRACTION100
5.81-62.3620.2281200.2042222X-RAY DIFFRACTION99.2373

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