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- PDB-6a01: The crystal structure of Mandelate oxidase Y128F with 3,3-difluor... -

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Basic information

Entry
Database: PDB / ID: 6a01
TitleThe crystal structure of Mandelate oxidase Y128F with 3,3-difluoro-2,2-dihydroxy-3-phenylpropionic 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 / L-lactate dehydrogenase activity / 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
3,3-difluoro-2,2-dihydroxy-3-phenylpropanoic acid / FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.868 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 5, 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)40,7043
Polymers40,0301
Non-polymers6742
Water5,152286
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)162,81612
Polymers160,1184
Non-polymers2,6988
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 area13670 Å2
ΔGint-105 kcal/mol
Surface area44310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.204, 138.204, 111.807
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-9NO / 3,3-difluoro-2,2-dihydroxy-3-phenylpropanoic acid


Mass: 218.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8F2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.5 Å3/Da / Density % sol: 64.85 %
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: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 44882 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4415 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 1.868→28.145 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17
RfactorNum. reflection% reflection
Rfree0.1996 2187 5.01 %
Rwork0.168 --
obs0.1695 43647 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.868→28.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2486 0 46 287 2819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052696
X-RAY DIFFRACTIONf_angle_d0.9173694
X-RAY DIFFRACTIONf_dihedral_angle_d12.662991
X-RAY DIFFRACTIONf_chiral_restr0.036423
X-RAY DIFFRACTIONf_plane_restr0.004485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8679-1.90850.26491090.22462030X-RAY DIFFRACTION77
1.9085-1.95290.27631350.20952221X-RAY DIFFRACTION86
1.9529-2.00170.22141280.20252487X-RAY DIFFRACTION94
2.0017-2.05580.24041300.20152595X-RAY DIFFRACTION99
2.0558-2.11630.27071360.19372644X-RAY DIFFRACTION100
2.1163-2.18450.20871420.1912617X-RAY DIFFRACTION100
2.1845-2.26260.22951480.18692643X-RAY DIFFRACTION100
2.2626-2.35310.22571380.18322649X-RAY DIFFRACTION100
2.3531-2.46020.2261580.17942629X-RAY DIFFRACTION100
2.4602-2.58980.2041400.17852652X-RAY DIFFRACTION100
2.5898-2.75190.17561200.17332684X-RAY DIFFRACTION100
2.7519-2.96420.23561280.17342700X-RAY DIFFRACTION100
2.9642-3.26210.17931300.15972661X-RAY DIFFRACTION100
3.2621-3.73320.17971490.1482707X-RAY DIFFRACTION100
3.7332-4.69990.17131460.13582725X-RAY DIFFRACTION100
4.6999-28.14850.16351500.15562816X-RAY DIFFRACTION99

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