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- PDB-6a1b: Mandelate oxidase mutant-Y128F with 3,3,3-trifluoro-2,2-dihydroxy... -

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Basic information

Entry
Database: PDB / ID: 6a1b
TitleMandelate oxidase mutant-Y128F with 3,3,3-trifluoro-2,2-dihydroxypropanoic 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
3,3,3-trifluoro-2,2-dihydroxypropanoic acid / FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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 7, 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)40,6463
Polymers40,0301
Non-polymers6162
Water6,485360
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)162,58412
Polymers160,1184
Non-polymers2,4668
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 area13960 Å2
ΔGint-106 kcal/mol
Surface area43090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.546, 137.546, 112.034
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-9O3 / 3,3,3-trifluoro-2,2-dihydroxypropanoic acid


Mass: 160.049 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H3F3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: Aug 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→30 Å / Num. obs: 90676 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.014 / Χ2: 0.953 / Net I/σ(I): 49.2
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8946 / CC1/2: 0.843 / Rpim(I) all: 0.27 / Rrim(I) all: 0.901 / Χ2: 0.8 / % possible all: 99.9

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Processing

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

3sgz


Resolution: 1.47→30 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1843 4419 5.01 %
Rwork0.1632 --
obs0.1642 88157 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 41 360 2894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182733
X-RAY DIFFRACTIONf_angle_d1.5083753
X-RAY DIFFRACTIONf_dihedral_angle_d8.9311510
X-RAY DIFFRACTIONf_chiral_restr0.122434
X-RAY DIFFRACTIONf_plane_restr0.009494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.469-1.48570.24481080.22391979X-RAY DIFFRACTION70
1.4857-1.50310.26611080.22962231X-RAY DIFFRACTION79
1.5031-1.52150.24071430.21092406X-RAY DIFFRACTION85
1.5215-1.54070.21961200.20982597X-RAY DIFFRACTION90
1.5407-1.5610.2541190.19882726X-RAY DIFFRACTION95
1.561-1.58240.21551330.19852772X-RAY DIFFRACTION97
1.5824-1.6050.21071650.19972802X-RAY DIFFRACTION99
1.605-1.62890.22271730.19172800X-RAY DIFFRACTION99
1.6289-1.65440.21011630.1832816X-RAY DIFFRACTION100
1.6544-1.68150.21541450.17862826X-RAY DIFFRACTION100
1.6815-1.71050.1841520.17332850X-RAY DIFFRACTION100
1.7105-1.74160.18721460.18362878X-RAY DIFFRACTION100
1.7416-1.77510.20051460.1822852X-RAY DIFFRACTION100
1.7751-1.81130.18311590.18022890X-RAY DIFFRACTION100
1.8113-1.85070.23151320.17382832X-RAY DIFFRACTION100
1.8507-1.89370.1811490.17322853X-RAY DIFFRACTION100
1.8937-1.94110.2051530.17192893X-RAY DIFFRACTION100
1.9411-1.99350.21721450.1662859X-RAY DIFFRACTION100
1.9935-2.05220.19831550.16812835X-RAY DIFFRACTION100
2.0522-2.11840.16731780.16452885X-RAY DIFFRACTION100
2.1184-2.19410.19831430.16132848X-RAY DIFFRACTION100
2.1941-2.28190.16831580.1592867X-RAY DIFFRACTION100
2.2819-2.38570.17751460.15372901X-RAY DIFFRACTION100
2.3857-2.51130.17031420.16122873X-RAY DIFFRACTION100
2.5113-2.66860.20171420.15892926X-RAY DIFFRACTION100
2.6686-2.87440.17211640.15932889X-RAY DIFFRACTION100
2.8744-3.16320.19021700.15642892X-RAY DIFFRACTION100
3.1632-3.620.15461540.14492953X-RAY DIFFRACTION100
3.62-4.55710.15271460.12982941X-RAY DIFFRACTION100
4.5571-26.720.17031620.16373066X-RAY DIFFRACTION99

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