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- PDB-6a23: Mandelate oxidase mutant-Y128F with the N5-benzyl-FMN adduct -

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Basic information

Entry
Database: PDB / ID: 6a23
TitleMandelate oxidase mutant-Y128F with the N5-benzyl-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 class I / Aldolase-type TIM barrel / TIM Barrel ...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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BENZOYL-FORMIC ACID / Chem-9OU / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level.
Authors: Lyu, S.Y. / Lin, K.H. / Yeh, H.W. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L.
History
DepositionJun 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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)40,7664
Polymers40,0301
Non-polymers7373
Water5,386299
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)163,06616
Polymers160,1184
Non-polymers2,94812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area11860 Å2
ΔGint-99 kcal/mol
Surface area43820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.843, 137.843, 111.840
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-9OU / 1-[5-(benzenecarbonyl)-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-1-deoxy-5-O-phosphono-D-ribitol


Mass: 562.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H27N4O10P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 3.51 Å3/Da / Density % sol: 64.94 %
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: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. obs: 63389 / % possible obs: 99.3 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.022 / Χ2: 0.952 / Net I/σ(I): 28.41
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.97 / Num. unique obs: 6271 / CC1/2: 0.77 / Rpim(I) all: 0.303 / Χ2: 0.779 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.11.1_2575)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.437 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18139 3035 5.1 %RANDOM
Rwork0.15523 ---
obs0.15656 56778 93.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0 Å2
2---0.18 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2485 0 51 299 2835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192716
X-RAY DIFFRACTIONr_bond_other_d0.0010.022617
X-RAY DIFFRACTIONr_angle_refined_deg2.5351.993717
X-RAY DIFFRACTIONr_angle_other_deg0.91435997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.85221.983116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38515435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3811535
X-RAY DIFFRACTIONr_chiral_restr0.1110.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
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_it1.871.611383
X-RAY DIFFRACTIONr_mcbond_other1.8571.6071382
X-RAY DIFFRACTIONr_mcangle_it2.8312.3961739
X-RAY DIFFRACTIONr_mcangle_other2.8342.41740
X-RAY DIFFRACTIONr_scbond_it2.9962.1091332
X-RAY DIFFRACTIONr_scbond_other2.9952.111333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.743.011967
X-RAY DIFFRACTIONr_long_range_B_refined6.62521.4513202
X-RAY DIFFRACTIONr_long_range_B_other6.62421.4513203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.654→1.697 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 163 -
Rwork0.226 3228 -
obs--72.46 %

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