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- PDB-6a13: Mandelate oxidase mutant-Y128F -

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Basic information

Entry
Database: PDB / ID: 6a13
TitleMandelate oxidase mutant-Y128F
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
FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLi, T.L. / Lin, K.H.
Citation
Journal: 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.
#1: Journal: 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 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Nov 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)40,4862
Polymers40,0301
Non-polymers4561
Water5,603311
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)161,9448
Polymers160,1184
Non-polymers1,8254
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 area13890 Å2
ΔGint-97 kcal/mol
Surface area43420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.468, 137.468, 111.995
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 3.49 Å3/Da / Density % sol: 64.8 %
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: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 58807 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.018 / Χ2: 0.934 / Net I/σ(I): 41.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5778 / CC1/2: 0.88 / Rpim(I) all: 0.253 / Χ2: 0.934 / % possible all: 100

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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: 1.7→30 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.83
RfactorNum. reflection% reflection
Rfree0.1968 3019 5.15 %
Rwork0.1748 --
obs0.176 58599 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 31 312 2820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182568
X-RAY DIFFRACTIONf_angle_d1.4863496
X-RAY DIFFRACTIONf_dihedral_angle_d11.7542055
X-RAY DIFFRACTIONf_chiral_restr0.11403
X-RAY DIFFRACTIONf_plane_restr0.009455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.72640.31691250.24322377X-RAY DIFFRACTION94
1.7264-1.75470.25091460.23042437X-RAY DIFFRACTION98
1.7547-1.7850.23751280.21562488X-RAY DIFFRACTION99
1.785-1.81740.22561280.20762507X-RAY DIFFRACTION100
1.8174-1.85240.23311080.19982533X-RAY DIFFRACTION100
1.8524-1.89020.21251470.19472503X-RAY DIFFRACTION100
1.8902-1.93130.23441730.18892488X-RAY DIFFRACTION100
1.9313-1.97620.22971540.19182479X-RAY DIFFRACTION100
1.9762-2.02560.20641270.18252521X-RAY DIFFRACTION100
2.0256-2.08040.21211640.1862504X-RAY DIFFRACTION100
2.0804-2.14160.21011450.1762487X-RAY DIFFRACTION100
2.1416-2.21070.17911270.17492542X-RAY DIFFRACTION100
2.2107-2.28960.24111380.17732546X-RAY DIFFRACTION100
2.2896-2.38130.18731120.17372522X-RAY DIFFRACTION100
2.3813-2.48960.19961570.18062532X-RAY DIFFRACTION100
2.4896-2.62080.19211150.17982545X-RAY DIFFRACTION100
2.6208-2.78480.18331290.17022542X-RAY DIFFRACTION100
2.7848-2.99970.18841380.17532567X-RAY DIFFRACTION100
2.9997-3.30110.18191330.1642587X-RAY DIFFRACTION100
3.3011-3.77790.16921440.15422549X-RAY DIFFRACTION100
3.7779-4.75640.16241360.13942610X-RAY DIFFRACTION100
4.7564-28.94660.18221450.17362714X-RAY DIFFRACTION99

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