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- PDB-6a11: Mandelate oxidase mutant-Y128F with phenylpyruvic acid -

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Basic information

Entry
Database: PDB / ID: 6a11
TitleMandelate oxidase mutant-Y128F with phenylpyruvic acid
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
FLAVIN MONONUCLEOTIDE / 3-PHENYLPYRUVIC ACID / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Biochemical and structural explorations of alpha-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction.
Authors: Yeh, H.W. / Lin, K.H. / Lyu, S.Y. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L.
History
DepositionJun 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 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)40,6503
Polymers40,0301
Non-polymers6212
Water6,431357
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)162,60012
Polymers160,1184
Non-polymers2,4828
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 area15530 Å2
ΔGint-77 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.485, 138.485, 111.539
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PPY / 3-PHENYLPYRUVIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 3.53 Å3/Da / Density % sol: 65.17 %
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: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 95758 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.017 / Χ2: 1.012 / Net I/σ(I): 42
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 9449 / CC1/2: 0.851 / Rpim(I) all: 0.27 / Χ2: 0.728 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AL7

1al7


Resolution: 1.45→30 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.74
RfactorNum. reflection% reflection
Rfree0.1907 4487 4.88 %
Rwork0.168 --
obs0.1691 91944 95.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 43 357 2893
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162787
X-RAY DIFFRACTIONf_angle_d1.4333825
X-RAY DIFFRACTIONf_dihedral_angle_d13.3332001
X-RAY DIFFRACTIONf_chiral_restr0.124435
X-RAY DIFFRACTIONf_plane_restr0.009511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4455-1.46190.28241040.23671935X-RAY DIFFRACTION64
1.4619-1.47910.19921210.21752085X-RAY DIFFRACTION70
1.4791-1.49720.2131060.2142239X-RAY DIFFRACTION74
1.4972-1.51610.221190.21262441X-RAY DIFFRACTION81
1.5161-1.53610.22881280.21362626X-RAY DIFFRACTION87
1.5361-1.55710.21951610.21542904X-RAY DIFFRACTION96
1.5571-1.57940.23231590.21062973X-RAY DIFFRACTION99
1.5794-1.60290.20741530.20173028X-RAY DIFFRACTION100
1.6029-1.6280.23511650.20542994X-RAY DIFFRACTION100
1.628-1.65470.25031310.19993043X-RAY DIFFRACTION100
1.6547-1.68320.22791760.19363019X-RAY DIFFRACTION100
1.6832-1.71380.20391520.19113027X-RAY DIFFRACTION100
1.7138-1.74680.21151420.19693027X-RAY DIFFRACTION100
1.7468-1.78240.24081460.19193024X-RAY DIFFRACTION100
1.7824-1.82120.231470.18693056X-RAY DIFFRACTION100
1.8212-1.86350.19941550.18743015X-RAY DIFFRACTION100
1.8635-1.91010.23771370.18183049X-RAY DIFFRACTION100
1.9101-1.96170.19631570.18113038X-RAY DIFFRACTION100
1.9617-2.01950.18671700.16973043X-RAY DIFFRACTION100
2.0195-2.08460.18261430.17183047X-RAY DIFFRACTION100
2.0846-2.15910.18831690.16443008X-RAY DIFFRACTION100
2.1591-2.24550.17381670.16473061X-RAY DIFFRACTION100
2.2455-2.34770.18041820.16393037X-RAY DIFFRACTION100
2.3477-2.47140.1821600.16713042X-RAY DIFFRACTION100
2.4714-2.62610.18681580.16293078X-RAY DIFFRACTION100
2.6261-2.82870.20331560.15563068X-RAY DIFFRACTION100
2.8287-3.1130.18571570.16193082X-RAY DIFFRACTION100
3.113-3.56270.16061570.14313108X-RAY DIFFRACTION100
3.5627-4.48570.14561430.12883158X-RAY DIFFRACTION100
4.4857-28.17610.19591660.16123202X-RAY DIFFRACTION98

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