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- PDB-5zzz: The crystal structure of Mandelate oxidase Y128C with benzoyl-for... -

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Basic information

Entry
Database: PDB / ID: 5zzz
TitleThe crystal structure of Mandelate oxidase Y128C 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 / 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: 1.446 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 5, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)40,6083
Polymers40,0021
Non-polymers6062
Water6,377354
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)162,43212
Polymers160,0064
Non-polymers2,4268
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 area15550 Å2
ΔGint-112 kcal/mol
Surface area43160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.229, 138.229, 112.134
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: 40001.531 Da / Num. of mol.: 1 / Mutation: Y128C
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-173 / BENZOYL-FORMIC ACID / OXO(PHENYL)ACETIC ACID


Mass: 150.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.51 Å3/Da / Density % sol: 64.99 %
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: Oct 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.446→30 Å / Num. obs: 95971 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 33.5
Reflection shellResolution: 1.446→1.5 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 9495 / % 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: 1.446→27.109 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.27
RfactorNum. reflection% reflection
Rfree0.1922 4766 5.09 %
Rwork0.1748 --
obs0.1757 93717 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.446→27.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2473 0 42 357 2872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012565
X-RAY DIFFRACTIONf_angle_d1.33489
X-RAY DIFFRACTIONf_dihedral_angle_d14.983919
X-RAY DIFFRACTIONf_chiral_restr0.057401
X-RAY DIFFRACTIONf_plane_restr0.006455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4461-1.46250.27231070.22812084X-RAY DIFFRACTION69
1.4625-1.47970.23931220.22362367X-RAY DIFFRACTION79
1.4797-1.49780.22611440.22052617X-RAY DIFFRACTION87
1.4978-1.51670.23541530.21892820X-RAY DIFFRACTION94
1.5167-1.53670.24041660.22022960X-RAY DIFFRACTION98
1.5367-1.55770.22041570.2112998X-RAY DIFFRACTION99
1.5577-1.580.26121720.20532991X-RAY DIFFRACTION100
1.58-1.60360.1971610.19673020X-RAY DIFFRACTION100
1.6036-1.62860.21451680.19312990X-RAY DIFFRACTION100
1.6286-1.65530.22591690.18893022X-RAY DIFFRACTION100
1.6553-1.68380.20941640.19013009X-RAY DIFFRACTION100
1.6838-1.71450.20271680.18733007X-RAY DIFFRACTION100
1.7145-1.74740.23051790.1933001X-RAY DIFFRACTION100
1.7474-1.78310.21081470.19583035X-RAY DIFFRACTION100
1.7831-1.82180.22451660.19353020X-RAY DIFFRACTION100
1.8218-1.86420.22251480.19293039X-RAY DIFFRACTION100
1.8642-1.91080.23221660.19013043X-RAY DIFFRACTION100
1.9108-1.96250.20321690.18232994X-RAY DIFFRACTION100
1.9625-2.02020.19251530.17663041X-RAY DIFFRACTION100
2.0202-2.08540.19781670.1743045X-RAY DIFFRACTION100
2.0854-2.15990.18231660.17243034X-RAY DIFFRACTION100
2.1599-2.24630.19491690.16653039X-RAY DIFFRACTION100
2.2463-2.34850.15341640.17013053X-RAY DIFFRACTION100
2.3485-2.47230.19571570.17473039X-RAY DIFFRACTION100
2.4723-2.6270.19921700.17873057X-RAY DIFFRACTION100
2.627-2.82970.17141560.16923073X-RAY DIFFRACTION100
2.8297-3.11410.19861420.17613092X-RAY DIFFRACTION100
3.1141-3.56380.17591570.15933104X-RAY DIFFRACTION100
3.5638-4.48670.15331620.14593131X-RAY DIFFRACTION100
4.4867-27.11370.17411770.15623226X-RAY DIFFRACTION99

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