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- PDB-6a4h: Mandelate oxidase mutant-Y128F with the peroxide FMN adduct -

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Basic information

Entry
Database: PDB / ID: 6a4h
TitleMandelate oxidase mutant-Y128F with the peroxide FMN adduct
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-9QF / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 19, 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)40,5202
Polymers40,0301
Non-polymers4901
Water2,288127
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)162,0808
Polymers160,1184
Non-polymers1,9614
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 area10050 Å2
ΔGint-83 kcal/mol
Surface area44560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.829, 138.829, 107.523
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-9QF / [(2~{R},3~{S},4~{S})-5-[(4~{a}~{S})-4~{a}-(dioxidanyl)-7,8-dimethyl-2,4-bis(oxidanylidene)-5~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] dihydrogen phosphate


Mass: 490.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.24 Å3/Da / Density % sol: 61.99 %
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: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 35949 / % possible obs: 99.4 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.016 / Χ2: 0.963 / Net I/σ(I): 40.6
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 3461 / CC1/2: 0.858 / Rpim(I) all: 0.226 / Χ2: 0.904 / % possible all: 97.7

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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: 1.99→29.159 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1719 4.97 %RANDOM
Rwork0.2176 ---
obs0.2188 34562 95.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.99→29.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 33 127 2572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052490
X-RAY DIFFRACTIONf_angle_d0.8363392
X-RAY DIFFRACTIONf_dihedral_angle_d6.8382036
X-RAY DIFFRACTIONf_chiral_restr0.05397
X-RAY DIFFRACTIONf_plane_restr0.006444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9904-2.0490.33861200.27762131X-RAY DIFFRACTION76
2.049-2.11510.28761240.26212432X-RAY DIFFRACTION86
2.1151-2.19070.28711160.252599X-RAY DIFFRACTION91
2.1907-2.27830.25961220.25512763X-RAY DIFFRACTION97
2.2783-2.3820.25721450.2342843X-RAY DIFFRACTION100
2.382-2.50750.24641580.2442823X-RAY DIFFRACTION100
2.5075-2.66450.26931470.23762849X-RAY DIFFRACTION100
2.6645-2.87010.25321540.22732831X-RAY DIFFRACTION100
2.8701-3.15860.25971740.22042828X-RAY DIFFRACTION100
3.1586-3.61490.22751500.20382864X-RAY DIFFRACTION99
3.6149-4.55160.19711580.18592877X-RAY DIFFRACTION99
4.5516-29.1620.21911510.19653003X-RAY DIFFRACTION98

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