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- PDB-6zq0: Structure of a-l-AraAZI-Bound MgGH51 a-L-Arabinofuranosidase Crys... -

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Basic information

Entry
Database: PDB / ID: 6zq0
TitleStructure of a-l-AraAZI-Bound MgGH51 a-L-Arabinofuranosidase Crystal Type 1
ComponentsMgGH51
KeywordsHYDROLASE / arabinofuranosidse / glycosidase / GH51 / cyclohellitol
Function / homologyChem-LXE
Function and homology information
Biological speciesMeripilus giganteus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 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 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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)69,7317
Polymers67,6881
Non-polymers2,0436
Water11,674648
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint18 kcal/mol
Surface area22330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.050, 65.460, 191.820
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, 650 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LXE / [(1~{S},2~{S},3~{S},4~{S})-2-(hydroxymethyl)-3,4-bis(oxidanyl)cyclopentyl]azanium


Mass: 148.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
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: 1.54→61.95 Å / Num. obs: 110936 / % possible obs: 99.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 18.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.043 / Net I/σ(I): 10.6
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 5472 / CC1/2: 0.505 / Rpim(I) all: 0.731 / % possible all: 99.7

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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: 1.54→61.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.02 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.073 / ESU R Free: 0.074
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2058 5515 4.976 %
Rwork0.1786 105323 -
all0.18 --
obs-110838 99.942 %
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: 19.586 Å2
Baniso -1Baniso -2Baniso -3
1-1.685 Å2-0 Å20 Å2
2---2.031 Å2-0 Å2
3---0.346 Å2
Refinement stepCycle: LAST / Resolution: 1.54→61.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 134 648 5542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135115
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174409
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.6837044
X-RAY DIFFRACTIONr_angle_other_deg1.5281.59310268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5485649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88323.305236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22615679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8061518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
X-RAY DIFFRACTIONr_nbd_refined0.2040.21034
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24412
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22601
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2565
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.110.22
X-RAY DIFFRACTIONr_nbd_other0.1390.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2620.230
X-RAY DIFFRACTIONr_mcbond_it1.4161.982545
X-RAY DIFFRACTIONr_mcbond_other1.4161.982544
X-RAY DIFFRACTIONr_mcangle_it1.8922.973190
X-RAY DIFFRACTIONr_mcangle_other1.8922.9713191
X-RAY DIFFRACTIONr_scbond_it2.1262.1552570
X-RAY DIFFRACTIONr_scbond_other2.1262.1552571
X-RAY DIFFRACTIONr_scangle_it2.9783.1793847
X-RAY DIFFRACTIONr_scangle_other2.9783.1793848
X-RAY DIFFRACTIONr_lrange_it3.99825.0966048
X-RAY DIFFRACTIONr_lrange_other3.81224.4795859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.3143850.3217706X-RAY DIFFRACTION99.8519
1.58-1.6230.3093820.3017514X-RAY DIFFRACTION99.9747
1.623-1.670.2753790.2677324X-RAY DIFFRACTION99.987
1.67-1.7220.263910.2377069X-RAY DIFFRACTION100
1.722-1.7780.2423610.2196886X-RAY DIFFRACTION99.9586
1.778-1.8410.2353460.2026681X-RAY DIFFRACTION100
1.841-1.910.2493360.1966441X-RAY DIFFRACTION99.9705
1.91-1.9880.2193360.1836211X-RAY DIFFRACTION100
1.988-2.0760.1983130.1775920X-RAY DIFFRACTION100
2.076-2.1780.213010.1665734X-RAY DIFFRACTION100
2.178-2.2960.2012790.1595405X-RAY DIFFRACTION99.9824
2.296-2.4350.1782650.1455189X-RAY DIFFRACTION100
2.435-2.6030.1882580.1434850X-RAY DIFFRACTION99.9804
2.603-2.8110.1712380.1444536X-RAY DIFFRACTION99.9791
2.811-3.080.1972210.1624179X-RAY DIFFRACTION99.9773
3.08-3.4430.2031920.1923816X-RAY DIFFRACTION100
3.443-3.9750.1881970.1783358X-RAY DIFFRACTION99.9719
3.975-4.8680.1551650.1332879X-RAY DIFFRACTION99.9672
4.868-6.8830.1851050.1632285X-RAY DIFFRACTION99.9164
6.883-62.0290.292650.2011340X-RAY DIFFRACTION99.4338

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