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- PDB-6zpy: Structure of Arabinose-Bound MgGH51 a-L-Arabinofuranosidase Cryst... -

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Basic information

Entry
Database: PDB / ID: 6zpy
TitleStructure of Arabinose-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51 / arabinose
Function / homologyalpha-L-arabinofuranose / NITRATE ION
Function and homology information
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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 1.3Nov 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
AAA: MgGH51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,98111
Polymers67,6881
Non-polymers2,29310
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint23 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.708, 65.043, 174.122
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 , 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, 5 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.: 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: Sugar ChemComp-AHR / alpha-L-arabinofuranose / alpha-L-arabinose / L-arabinose / arabinose


Type: L-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LArafaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-arabinofuranoseCOMMON NAMEGMML 1.0
a-L-ArafIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AraSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 823 molecules

#5: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.75 %
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: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 1.27→65.04 Å / Num. obs: 176357 / % possible obs: 98.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.14 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.04 / Net I/σ(I): 8.7
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 8584 / CC1/2: 0.764 / Rpim(I) all: 0.374 / % possible all: 97.3

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Processing

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

6zps


Resolution: 1.27→56.544 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.265 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 8652 4.91 %
Rwork0.1394 167555 -
all0.141 --
obs-176207 98.391 %
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: 14.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0 Å20 Å2
2--0.705 Å2-0 Å2
3----0.235 Å2
Refinement stepCycle: LAST / Resolution: 1.27→56.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 150 818 5743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0135157
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174440
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.6857095
X-RAY DIFFRACTIONr_angle_other_deg1.6411.59210349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1925652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10323.402241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61615695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0861518
X-RAY DIFFRACTIONr_chiral_restr0.1050.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021107
X-RAY DIFFRACTIONr_nbd_refined0.2070.21079
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.24589
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22618
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.22576
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2625
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0330.26
X-RAY DIFFRACTIONr_nbd_other0.1350.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.241
X-RAY DIFFRACTIONr_mcbond_it1.51.4022545
X-RAY DIFFRACTIONr_mcbond_other1.51.4012544
X-RAY DIFFRACTIONr_mcangle_it1.7452.1193191
X-RAY DIFFRACTIONr_mcangle_other1.7452.1193192
X-RAY DIFFRACTIONr_scbond_it2.2261.6052612
X-RAY DIFFRACTIONr_scbond_other2.2141.6022597
X-RAY DIFFRACTIONr_scangle_it2.5682.3533895
X-RAY DIFFRACTIONr_scangle_other2.5512.3483881
X-RAY DIFFRACTIONr_lrange_it2.80118.9056202
X-RAY DIFFRACTIONr_lrange_other2.51718.0455960
X-RAY DIFFRACTIONr_rigid_bond_restr3.02439597
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.3030.3065930.29312126X-RAY DIFFRACTION96.8476
1.303-1.3390.2556160.25411793X-RAY DIFFRACTION97.2187
1.339-1.3770.2446340.22611492X-RAY DIFFRACTION97.4132
1.377-1.420.2216110.19711176X-RAY DIFFRACTION97.5099
1.42-1.4660.2265960.1810900X-RAY DIFFRACTION98.0553
1.466-1.5180.2025370.15710543X-RAY DIFFRACTION97.9491
1.518-1.5750.1895090.1310298X-RAY DIFFRACTION98.0494
1.575-1.6390.1654850.129860X-RAY DIFFRACTION98.402
1.639-1.7120.1695250.1079455X-RAY DIFFRACTION98.2961
1.712-1.7960.1624650.1039144X-RAY DIFFRACTION99.1129
1.796-1.8930.1614440.1118689X-RAY DIFFRACTION98.7992
1.893-2.0080.1813980.1328287X-RAY DIFFRACTION99.0647
2.008-2.1470.1744500.1137758X-RAY DIFFRACTION99.3464
2.147-2.3180.1813830.1347257X-RAY DIFFRACTION99.4533
2.318-2.540.1513560.1066702X-RAY DIFFRACTION99.6893
2.54-2.8390.1612980.1136183X-RAY DIFFRACTION99.8306
2.839-3.2790.1572460.1325457X-RAY DIFFRACTION99.8599
3.279-4.0150.1722110.1464680X-RAY DIFFRACTION99.9387
4.015-5.6770.1461930.1243632X-RAY DIFFRACTION99.9216
5.677-56.5440.2261020.1922123X-RAY DIFFRACTION99.4191

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