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- PDB-4mah: Structure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxy... -

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Basic information

Entry
Database: PDB / ID: 4mah
TitleStructure of Aspergillus oryzae AA11 Lytic Polysaccharide Monooxygenase with Zn
ComponentsAA11 Lytic Polysaccharide Monooxygenase
KeywordsOXIDOREDUCTASE / chitin oxidation / GH61 / AA11 / chitin degradation
Function / homologyCoagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å
AuthorsHemsworth, G.R. / Henrissat, B. / Walton, P.H. / Davies, G.J.
CitationJournal: Nat.Chem.Biol. / Year: 2014
Title: Discovery and characterization of a new family of lytic polysaccharide monooxygenases.
Authors: Hemsworth, G.R. / Henrissat, B. / Davies, G.J. / Walton, P.H.
History
DepositionAug 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Source and taxonomy
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Feb 5, 2014Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AA11 Lytic Polysaccharide Monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2414
Polymers23,0781
Non-polymers1633
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.207, 61.498, 65.136
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 AA11 Lytic Polysaccharide Monooxygenase


Mass: 23077.838 Da / Num. of mol.: 1 / Fragment: UNP residues 20-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: AO090102000501 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21*(DE3)
References: UniProt: Q2UA85, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#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.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 6
Details: 10 mM zinc chloride, 100 mM MES, pH 6.0, 20% w/v PEG6000, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 1.55→28.07 Å / Num. all: 32367 / Num. obs: 32367 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.03 / Net I/σ(I): 17.7
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1499 / % possible all: 94.2

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Processing

Software
NameVersionClassificationNB
SCALA0.1.29data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.55→28.07 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1671 / WRfactor Rwork: 0.1337 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9126 / SU B: 2.101 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0632 / SU Rfree: 0.0587 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1656 1619 5 %RANDOM
Rwork0.132 ---
all0.1337 32310 --
obs0.1337 32310 98.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.07 Å2 / Biso mean: 20.2941 Å2 / Biso min: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.55→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1372 0 6 147 1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021424
X-RAY DIFFRACTIONr_bond_other_d0.0020.021276
X-RAY DIFFRACTIONr_angle_refined_deg1.421.951948
X-RAY DIFFRACTIONr_angle_other_deg0.9653.0042940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32825.17258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.89215203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.309155
X-RAY DIFFRACTIONr_chiral_restr0.0890.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211660
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02313
X-RAY DIFFRACTIONr_mcbond_it4.4131.726747
X-RAY DIFFRACTIONr_mcbond_other4.4061.724746
X-RAY DIFFRACTIONr_mcangle_it4.4952.579930
X-RAY DIFFRACTIONr_rigid_bond_restr10.36432700
X-RAY DIFFRACTIONr_sphericity_free27.17544
X-RAY DIFFRACTIONr_sphericity_bonded35.38152768
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 95 -
Rwork0.167 2189 -
all-2284 -
obs--95.56 %

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