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- PDB-6a36: Mandelate oxidase mutant-Y128F with the 3-fluoropyruvic acid FMN ... -

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Basic information

Entry
Database: PDB / ID: 6a36
TitleMandelate oxidase mutant-Y128F with the 3-fluoropyruvic acid FMN adduct
Components4-hydroxymandelate oxidase
KeywordsFLAVOPROTEIN / FMN-dependent oxidase
Function / homology
Function and homology information


4-hydroxymandelate oxidase / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / vancomycin biosynthetic process / FMN binding
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-9P9 / Chem-9PF / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: Protein Sci. / Year: 2020
Title: Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity.
Authors: Lin, K.H. / Lyu, S.Y. / Yeh, H.W. / Li, Y.S. / Hsu, N.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Wang, Z.C. / Wu, C.J. / Li, T.L.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: 4-hydroxymandelate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1563
Polymers40,0301
Non-polymers1,1272
Water6,269348
1
A: 4-hydroxymandelate oxidase
hetero molecules

A: 4-hydroxymandelate oxidase
hetero molecules

A: 4-hydroxymandelate oxidase
hetero molecules

A: 4-hydroxymandelate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,62612
Polymers160,1184
Non-polymers4,5078
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area9940 Å2
ΔGint-74 kcal/mol
Surface area43420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.749, 137.749, 111.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 4-hydroxymandelate oxidase


Mass: 40029.562 Da / Num. of mol.: 1 / Mutation: Y128F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Gene: hmo / Production host: Escherichia coli (E. coli) / References: UniProt: O52792, 4-hydroxymandelate oxidase
#2: Chemical ChemComp-9P9 / 1-{5-[(3S)-3-carboxy-4-fluoro-3-hydroxybutanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-1-deoxy-5-O-phosphono-D-ribitol


Mass: 606.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28FN4O13P
#3: Chemical ChemComp-9PF / 1-deoxy-1-{5-[(1S)-2-fluoro-1-hydroxyethyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-5-O-phosphono-D-ribitol


Mass: 520.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26FN4O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tascimate, 0.1M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→30 Å / Num. obs: 96402 / % possible obs: 100 % / Redundancy: 12 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.013 / Χ2: 0.97 / Net I/σ(I): 52.4
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3 / Num. unique obs: 9506 / CC1/2: 0.873 / Rpim(I) all: 0.241 / Χ2: 0.865 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 1.44→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.9 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19242 4708 5 %RANDOM
Rwork0.17607 ---
obs0.17688 89143 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.756 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2---0.07 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.44→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 76 350 2897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192673
X-RAY DIFFRACTIONr_bond_other_d0.0030.022563
X-RAY DIFFRACTIONr_angle_refined_deg1.651.9983660
X-RAY DIFFRACTIONr_angle_other_deg1.0413.0055878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.83322.162111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56515416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7021532
X-RAY DIFFRACTIONr_chiral_restr0.2450.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213040
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
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_it1.1671.5041363
X-RAY DIFFRACTIONr_mcbond_other1.1671.5041362
X-RAY DIFFRACTIONr_mcangle_it1.8772.2471706
X-RAY DIFFRACTIONr_mcangle_other1.8762.2471707
X-RAY DIFFRACTIONr_scbond_it1.8671.8591310
X-RAY DIFFRACTIONr_scbond_other1.8671.8591310
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9842.6771947
X-RAY DIFFRACTIONr_long_range_B_refined5.16620.2943194
X-RAY DIFFRACTIONr_long_range_B_other5.16520.2913195
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.44→1.477 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 236 -
Rwork0.244 5080 -
obs--75.47 %

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