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- PDB-6zq1: Structure of AraDNJ-Bound MgGH51 a-L-Arabinofuranosidase Crystal ... -

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Basic information

Entry
Database: PDB / ID: 6zq1
TitleStructure of AraDNJ-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51 / iminosugar
Function / homology1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL
Function and homology information
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: MgGH51
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7167
Polymers67,6881
Non-polymers2,0286
Water9,818545
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint18 kcal/mol
Surface area22760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.803, 65.914, 193.563
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 , 2 types, 4 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

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Non-polymers , 3 types, 547 molecules

#4: Chemical ChemComp-EDG / 1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL


Mass: 133.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 56.35 %
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 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→29.87 Å / Num. obs: 85172 / % possible obs: 99.9 % / Redundancy: 34.5 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.028 / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4409 / CC1/2: 0.915 / Rpim(I) all: 0.281 / % possible all: 99.4

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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: 1.7→29.87 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.779 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.098
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2165 4303 5.059 %
Rwork0.1946 80757 -
all0.196 --
obs-85060 99.894 %
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: 19.379 Å2
Baniso -1Baniso -2Baniso -3
1-4.511 Å20 Å20 Å2
2---1.955 Å20 Å2
3----2.556 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4767 0 133 545 5445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135076
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174378
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.6826977
X-RAY DIFFRACTIONr_angle_other_deg1.4351.5910188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6975636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74923.222239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87815677
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2661519
X-RAY DIFFRACTIONr_chiral_restr0.0810.2715
X-RAY DIFFRACTIONr_chiral_restr_other0.1030.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021099
X-RAY DIFFRACTIONr_nbd_refined0.1960.2925
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.23996
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22478
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2416
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1080.22
X-RAY DIFFRACTIONr_nbd_other0.0960.213
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3930.212
X-RAY DIFFRACTIONr_mcbond_it1.5371.9872517
X-RAY DIFFRACTIONr_mcbond_other1.5361.9862516
X-RAY DIFFRACTIONr_mcangle_it2.0572.9753147
X-RAY DIFFRACTIONr_mcangle_other2.0562.9763148
X-RAY DIFFRACTIONr_scbond_it1.9842.1462559
X-RAY DIFFRACTIONr_scbond_other1.9842.1462559
X-RAY DIFFRACTIONr_scangle_it2.8573.173825
X-RAY DIFFRACTIONr_scangle_other2.8573.1713826
X-RAY DIFFRACTIONr_lrange_it4.0324.2555692
X-RAY DIFFRACTIONr_lrange_other3.90423.9235571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3132640.2975920X-RAY DIFFRACTION99.3095
1.744-1.7920.3173080.2725727X-RAY DIFFRACTION99.9834
1.792-1.8440.252720.245624X-RAY DIFFRACTION100
1.844-1.9010.2453160.2225411X-RAY DIFFRACTION100
1.901-1.9630.2753080.2535233X-RAY DIFFRACTION100
1.963-2.0320.2422570.2035156X-RAY DIFFRACTION99.9815
2.032-2.1080.2312600.1954956X-RAY DIFFRACTION99.9808
2.108-2.1950.212460.1854758X-RAY DIFFRACTION100
2.195-2.2920.2262690.1944539X-RAY DIFFRACTION99.8132
2.292-2.4040.1892460.1624358X-RAY DIFFRACTION100
2.404-2.5340.212170.1654187X-RAY DIFFRACTION100
2.534-2.6880.2232110.1623934X-RAY DIFFRACTION99.9759
2.688-2.8730.2132220.173717X-RAY DIFFRACTION100
2.873-3.1030.2171760.1853479X-RAY DIFFRACTION100
3.103-3.40.2421690.2073213X-RAY DIFFRACTION99.9704
3.4-3.8010.2011580.2072921X-RAY DIFFRACTION99.9675
3.801-4.3880.1831490.1742603X-RAY DIFFRACTION99.9637
4.388-5.3740.1511150.1532221X-RAY DIFFRACTION99.9572
5.374-7.5970.185910.1761763X-RAY DIFFRACTION99.9461
7.597-29.870.193490.221037X-RAY DIFFRACTION99.8162

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