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- PDB-6zps: Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Ty... -

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Basic information

Entry
Database: PDB / ID: 6zps
TitleStructure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3 Collected at 2.75 A
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51 / Sulphur SAD
Function / homologyACETATE ION
Function and homology information
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.795 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 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 / _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)72,58238
Polymers67,6881
Non-polymers4,89437
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-156 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.171, 84.171, 257.347
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-934-

HOH

21AAA-1551-

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 , 5 types, 784 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / 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.: 13 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
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: Conductive cooling through pin / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.755 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: 2.755 Å / Relative weight: 1
ReflectionResolution: 1.79→257.35 Å / Num. obs: 74070 / % possible obs: 84.4 % / Redundancy: 70.2 % / CC1/2: 0.999 / Rpim(I) all: 0.012 / Net I/σ(I): 35.1
Reflection shellResolution: 1.79→1.8 Å / Redundancy: 21.5 % / Mean I/σ(I) obs: 5.7 / Num. unique obs: 4624 / CC1/2: 0.91 / Rpim(I) all: 0.142 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data processing
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.795→80.128 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.7 / SU ML: 0.053 / Cross valid method: FREE R-VALUE / ESU R: 0.099 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1784 3570 4.827 %
Rwork0.1438 70385 -
all0.145 --
obs-73955 84.529 %
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: 19.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.389 Å2-0 Å2-0 Å2
2--0.389 Å2-0 Å2
3----0.778 Å2
Refinement stepCycle: LAST / Resolution: 1.795→80.128 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 285 751 5826
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135351
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174582
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.6987387
X-RAY DIFFRACTIONr_angle_other_deg1.5141.60510706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0715667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41723.105248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99615715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8551521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021132
X-RAY DIFFRACTIONr_nbd_refined0.2310.2956
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.24194
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22611
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2820.2579
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.4810.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.212
X-RAY DIFFRACTIONr_nbd_other0.1960.238
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.244
X-RAY DIFFRACTIONr_mcbond_it1.5881.8342573
X-RAY DIFFRACTIONr_mcbond_other1.5851.8322570
X-RAY DIFFRACTIONr_mcangle_it2.1372.7423225
X-RAY DIFFRACTIONr_mcangle_other2.1372.7433226
X-RAY DIFFRACTIONr_scbond_it2.8062.1832778
X-RAY DIFFRACTIONr_scbond_other2.8052.1842779
X-RAY DIFFRACTIONr_scangle_it4.0093.1784146
X-RAY DIFFRACTIONr_scangle_other4.0083.1784147
X-RAY DIFFRACTIONr_lrange_it5.18124.1316088
X-RAY DIFFRACTIONr_lrange_other4.85323.2725862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.795-1.8410.2122700.165592X-RAY DIFFRACTION92.1264
1.841-1.8920.2011740.1553535X-RAY DIFFRACTION59.9483
1.892-1.9470.289980.2292246X-RAY DIFFRACTION38.7054
1.947-2.0070.2112220.1484454X-RAY DIFFRACTION79.7
2.007-2.0720.2042070.1484003X-RAY DIFFRACTION74.185
2.072-2.1450.1872460.1454756X-RAY DIFFRACTION90.5339
2.145-2.2260.1862520.1315086X-RAY DIFFRACTION100
2.226-2.3170.2141810.1463336X-RAY DIFFRACTION68.3842
2.317-2.420.1722530.1224710X-RAY DIFFRACTION100
2.42-2.5380.1652010.1224519X-RAY DIFFRACTION100
2.538-2.6750.1831780.1333489X-RAY DIFFRACTION81.7068
2.675-2.8380.182030.1383833X-RAY DIFFRACTION93.9041
2.838-3.0330.1712130.1473832X-RAY DIFFRACTION100
3.033-3.2760.1782020.1563558X-RAY DIFFRACTION100
3.276-3.5890.1691360.162975X-RAY DIFFRACTION89.2427
3.589-4.0130.1511410.1372509X-RAY DIFFRACTION82.8384
4.013-4.6330.1371330.1172693X-RAY DIFFRACTION100
4.633-5.6740.1491190.1252320X-RAY DIFFRACTION100
5.674-8.0220.195930.1731821X-RAY DIFFRACTION100
8.022-80.1280.268480.2011117X-RAY DIFFRACTION100

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