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- PDB-6a1l: Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleot... -

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Basic information

Entry
Database: PDB / ID: 6a1l
TitleMandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and benzoic 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
Chem-9O9 / BENZOIC ACID / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: 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.
History
DepositionJun 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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)40,7535
Polymers40,0301
Non-polymers7244
Water5,999333
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)163,01420
Polymers160,1184
Non-polymers2,89616
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 area13110 Å2
ΔGint-42 kcal/mol
Surface area43040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.721, 137.721, 111.585
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-9O9 / 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol


Mass: 455.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H22N3O9P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: Jan 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 104843 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.021 / Χ2: 1.003 / Net I/σ(I): 29.6
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10346 / CC1/2: 0.789 / Rpim(I) all: 0.31 / Χ2: 1.003 / % possible all: 100

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Processing

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

3sgz


Resolution: 1.4→30 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.95
RfactorNum. reflection% reflection
Rfree0.1855 5237 5 %
Rwork0.1752 --
obs0.1758 104841 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2477 0 50 335 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062680
X-RAY DIFFRACTIONf_angle_d0.9823665
X-RAY DIFFRACTIONf_dihedral_angle_d19.291984
X-RAY DIFFRACTIONf_chiral_restr0.209423
X-RAY DIFFRACTIONf_plane_restr0.005481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3982-1.41410.29571740.27953195X-RAY DIFFRACTION97
1.4141-1.43080.29041820.25613282X-RAY DIFFRACTION100
1.4308-1.44820.2761630.24243285X-RAY DIFFRACTION100
1.4482-1.46650.28921730.23323281X-RAY DIFFRACTION100
1.4665-1.48580.25361750.22893288X-RAY DIFFRACTION100
1.4858-1.50620.22451610.22253309X-RAY DIFFRACTION100
1.5062-1.52770.24281790.21263299X-RAY DIFFRACTION100
1.5277-1.55050.20931760.20793295X-RAY DIFFRACTION100
1.5505-1.57470.20761920.2043263X-RAY DIFFRACTION100
1.5747-1.60050.21531740.20083308X-RAY DIFFRACTION100
1.6005-1.62810.20871740.19293297X-RAY DIFFRACTION100
1.6281-1.65770.2011470.18613300X-RAY DIFFRACTION100
1.6577-1.68960.23631760.18713309X-RAY DIFFRACTION100
1.6896-1.72410.20531800.18663298X-RAY DIFFRACTION100
1.7241-1.76160.22941520.19243328X-RAY DIFFRACTION100
1.7616-1.80260.2051720.18563301X-RAY DIFFRACTION100
1.8026-1.84760.17251620.18253325X-RAY DIFFRACTION100
1.8476-1.89760.19511450.17793331X-RAY DIFFRACTION100
1.8976-1.95340.21421760.17833314X-RAY DIFFRACTION100
1.9534-2.01640.1961780.16893324X-RAY DIFFRACTION100
2.0164-2.08850.15651920.16993293X-RAY DIFFRACTION100
2.0885-2.17210.18071780.16243328X-RAY DIFFRACTION100
2.1721-2.27090.17521940.17043321X-RAY DIFFRACTION100
2.2709-2.39060.20771670.17253361X-RAY DIFFRACTION100
2.3906-2.54020.17911930.17633308X-RAY DIFFRACTION100
2.5402-2.73620.17341920.17313346X-RAY DIFFRACTION100
2.7362-3.01130.18951600.17473365X-RAY DIFFRACTION100
3.0113-3.44640.16721810.16223389X-RAY DIFFRACTION100
3.4464-4.33950.14851770.14483423X-RAY DIFFRACTION100
4.3395-28.06340.1661920.16723538X-RAY DIFFRACTION99

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