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- PDB-6a08: The crystal structure of Mandelate oxidase with benzoyl-formic acid -

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Basic information

Entry
Database: PDB / ID: 6a08
TitleThe crystal structure of Mandelate oxidase with benzoyl-formic 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
BENZOYL-FORMIC ACID / FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.547 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 5, 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)40,8265
Polymers40,0461
Non-polymers7814
Water5,909328
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)163,30620
Polymers160,1824
Non-polymers3,12416
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 area17520 Å2
ΔGint-172 kcal/mol
Surface area44060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.911, 137.911, 111.773
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: 40045.562 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 3.48 Å3/Da / Density % sol: 64.68 %
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 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.547→30 Å / Num. obs: 78018 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 43.2
Reflection shellResolution: 1.547→1.61 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7718 / % 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: 1.547→29.343 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3
RfactorNum. reflection% reflection
Rfree0.1861 3844 5.08 %
Rwork0.1641 --
obs0.1646 75720 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.547→29.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 54 329 2885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012812
X-RAY DIFFRACTIONf_angle_d1.2953854
X-RAY DIFFRACTIONf_dihedral_angle_d13.5921036
X-RAY DIFFRACTIONf_chiral_restr0.06438
X-RAY DIFFRACTIONf_plane_restr0.006513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.547-1.58570.24981090.21824039X-RAY DIFFRACTION75
1.5857-1.62860.23971240.21214544X-RAY DIFFRACTION85
1.6286-1.67650.2291420.2075236X-RAY DIFFRACTION98
1.6765-1.73060.2261450.1985351X-RAY DIFFRACTION100
1.7306-1.79250.21811460.18985370X-RAY DIFFRACTION100
1.7925-1.86420.22031460.18345398X-RAY DIFFRACTION100
1.8642-1.94910.20711460.17895378X-RAY DIFFRACTION100
1.9491-2.05180.20121470.16855403X-RAY DIFFRACTION100
2.0518-2.18030.19211470.1645403X-RAY DIFFRACTION100
2.1803-2.34860.17531470.16195442X-RAY DIFFRACTION100
2.3486-2.58480.19281470.16825441X-RAY DIFFRACTION100
2.5848-2.95850.17871500.16055487X-RAY DIFFRACTION100
2.9585-3.72620.17681490.1445511X-RAY DIFFRACTION100
3.7262-29.34830.14451550.1415717X-RAY DIFFRACTION100

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