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- PDB-8rpf: Crystal structure of an alcohol-oxidase from Sphingobacterium dae... -

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Basic information

Entry
Database: PDB / ID: 8rpf
TitleCrystal structure of an alcohol-oxidase from Sphingobacterium daejeonense
Componentsalcohol oxidase
KeywordsOXIDOREDUCTASE / ALCOHOL OXIDASE / SPHINGOBACTERIUM DAEJEONENSE / FLAVOPROTEIN
Function / homology1-BUTANOL / FLAVIN-ADENINE DINUCLEOTIDE / HEXANE-1,6-DIOL
Function and homology information
Biological speciesSphingobacterium daejeonense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez-Julvez, M. / Ferreira, P. / Cinca, P.
Funding support Spain, 2items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)TED2021-130803B-I00 Spain
Other governmentBiologia Estructural E35_23R
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
B: alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8548
Polymers121,8982
Non-polymers1,9566
Water13,331740
1
A: alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0015
Polymers60,9491
Non-polymers1,0524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alcohol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8533
Polymers60,9491
Non-polymers9042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.985, 76.780, 88.222
Angle α, β, γ (deg.)90.00, 98.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein alcohol oxidase


Mass: 60949.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobacterium daejeonense (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: aryl-alcohol oxidase
#2: Chemical ChemComp-1BO / 1-BUTANOL / BUTAN-1-OL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10%w/vPEG20000, 20%v/vPEGMME550 0.02Mof each alcohol 0.1MMES/imidazole pH6.5

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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 PILATUS3 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→87.29 Å / Num. obs: 71851 / % possible obs: 98.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 5.3 / Num. unique obs: 10383 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→64.34 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.714 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20791 3493 4.9 %RANDOM
Rwork0.16351 ---
obs0.16564 68336 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.656 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å2-0 Å20.24 Å2
2---1.49 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 2→64.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8394 0 10 740 9144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168009
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.8211671
X-RAY DIFFRACTIONr_angle_other_deg0.5451.75218501
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.93151068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.914539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.174101417
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.21295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210067
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021899
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_it2.6292.9064275
X-RAY DIFFRACTIONr_mcbond_other2.6292.9064275
X-RAY DIFFRACTIONr_mcangle_it3.5925.2115342
X-RAY DIFFRACTIONr_mcangle_other3.5925.2125343
X-RAY DIFFRACTIONr_scbond_it3.4213.254321
X-RAY DIFFRACTIONr_scbond_other3.4213.254322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1765.8056330
X-RAY DIFFRACTIONr_long_range_B_refined6.62530.929927
X-RAY DIFFRACTIONr_long_range_B_other6.56630.229754
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
Rfree0.253 250 -
Rwork0.191 5023 -
obs--97.36 %

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