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- PDB-8rpg: Crystal structure of an alcohol oxidase from Streptomyces hiroshi... -

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Basic information

Entry
Database: PDB / ID: 8rpg
TitleCrystal structure of an alcohol oxidase from Streptomyces hiroshimensis
ComponentsAlcohol oxidase
KeywordsOXIDOREDUCTASE / ALCOHOL OXIDASE / STREPTOMYCES HIROSHIMENSIS / FLAVOPROTEIN
Function / homologyFLAVIN-ADENINE DINUCLEOTIDE / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesStreptomyces hiroshimensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez-Julvez, M. / Ferreira, P. / Cinca-Fernando, P.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)TED2021-130803B-I00 Spain
Other governmentBiologia Estructural E35_23R Spain
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Discovery, characterization, and synthetic potential of two novel bacterial aryl-alcohol oxidases.
Authors: Cinca-Fernando, P. / Ascaso-Alegre, C. / Sevilla, E. / Martinez-Julvez, M. / Mangas-Sanchez, J. / Ferreira, P.
History
DepositionJan 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2189
Polymers56,7301
Non-polymers1,4888
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-4 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.510, 97.688, 68.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Alcohol oxidase


Mass: 56729.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces hiroshimensis (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: aryl-alcohol oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30 % Polyethylene glycol 4000 100 mM TRIS pH 8.5 200 mM Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→97.69 Å / Num. obs: 36978 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 5325

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→62.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.104 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19324 1898 5.1 %RANDOM
Rwork0.15102 ---
obs0.15317 35032 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å2-0 Å2
2---1.67 Å20 Å2
3---0.99 Å2
Refinement stepCycle: 1 / Resolution: 2→62.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 0 304 4225
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124010
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163747
X-RAY DIFFRACTIONr_angle_refined_deg1.6511.825470
X-RAY DIFFRACTIONr_angle_other_deg0.5731.7358590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.949546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1210552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024958
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02923
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0462.3952071
X-RAY DIFFRACTIONr_mcbond_other2.0432.3932070
X-RAY DIFFRACTIONr_mcangle_it2.7354.292587
X-RAY DIFFRACTIONr_mcangle_other2.7374.2922588
X-RAY DIFFRACTIONr_scbond_it3.4552.7841939
X-RAY DIFFRACTIONr_scbond_other3.4552.7841940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.184.9012884
X-RAY DIFFRACTIONr_long_range_B_refined8.33827.344496
X-RAY DIFFRACTIONr_long_range_B_other7.50826.014434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 130 -
Rwork0.165 2545 -
obs--99.96 %

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