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- PDB-5zzt: The crystal structure of Mandelate oxidase with 3,3-difluoro-2-hy... -

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Basic information

Entry
Database: PDB / ID: 5zzt
TitleThe crystal structure of Mandelate oxidase with 3,3-difluoro-2-hydroxy-3-phenylpropionic 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-9NL / FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 4, 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)40,7043
Polymers40,0461
Non-polymers6582
Water5,963331
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)162,81612
Polymers160,1824
Non-polymers2,6348
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 area13720 Å2
ΔGint-106 kcal/mol
Surface area43330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.738, 137.738, 111.788
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-9NL / (2R)-3,3-difluoro-2-hydroxy-3-phenylpropanoic acid


Mass: 202.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8F2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 3.47 Å3/Da / Density % sol: 64.59 %
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 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 116441 / % possible obs: 99.8 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 37.7
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 11550 / % 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: 1.35→29.317 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.24
RfactorNum. reflection% reflection
Rfree0.1898 5348 4.88 %
Rwork0.1736 --
obs0.1744 109621 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→29.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 45 334 2849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012768
X-RAY DIFFRACTIONf_angle_d1.2943797
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331036
X-RAY DIFFRACTIONf_chiral_restr0.054431
X-RAY DIFFRACTIONf_plane_restr0.007503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3501-1.36540.24841040.22922136X-RAY DIFFRACTION58
1.3654-1.38150.23681130.23612376X-RAY DIFFRACTION65
1.3815-1.39840.25471310.22242593X-RAY DIFFRACTION71
1.3984-1.41610.24911350.22262792X-RAY DIFFRACTION76
1.4161-1.43470.26291520.21662905X-RAY DIFFRACTION80
1.4347-1.45430.24221560.22143140X-RAY DIFFRACTION85
1.4543-1.47510.27121930.21793351X-RAY DIFFRACTION92
1.4751-1.49710.22441740.21473608X-RAY DIFFRACTION98
1.4971-1.52050.22271910.21313612X-RAY DIFFRACTION99
1.5205-1.54550.24631750.21043667X-RAY DIFFRACTION100
1.5455-1.57210.21981850.20613689X-RAY DIFFRACTION100
1.5721-1.60070.21441780.23694X-RAY DIFFRACTION100
1.6007-1.63150.17671790.19383678X-RAY DIFFRACTION100
1.6315-1.66480.21251920.19323676X-RAY DIFFRACTION100
1.6648-1.7010.18231900.18753703X-RAY DIFFRACTION100
1.701-1.74050.20631860.19253654X-RAY DIFFRACTION100
1.7405-1.78410.18962040.19133679X-RAY DIFFRACTION100
1.7841-1.83230.20881990.19113670X-RAY DIFFRACTION100
1.8323-1.88620.20091980.18383674X-RAY DIFFRACTION100
1.8862-1.94710.1971830.18273698X-RAY DIFFRACTION100
1.9471-2.01660.17961680.17833718X-RAY DIFFRACTION100
2.0166-2.09740.18971910.17473690X-RAY DIFFRACTION100
2.0974-2.19280.18081910.17283715X-RAY DIFFRACTION100
2.1928-2.30830.19072060.16893686X-RAY DIFFRACTION100
2.3083-2.45290.18842100.17053698X-RAY DIFFRACTION100
2.4529-2.64220.20021980.16833721X-RAY DIFFRACTION100
2.6422-2.90790.17391690.16713739X-RAY DIFFRACTION99
2.9079-3.32810.18311930.15853731X-RAY DIFFRACTION99
3.3281-4.19110.16951880.14073765X-RAY DIFFRACTION99
4.1911-29.32440.162160.15513815X-RAY DIFFRACTION97

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