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- PDB-5zzs: The crystal structure of Mandelate oxidase with benzoic acid -

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Basic information

Entry
Database: PDB / ID: 5zzs
TitleThe crystal structure of Mandelate oxidase with 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
BENZOIC ACID / FLAVIN MONONUCLEOTIDE / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.398 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: 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 4, 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 1.2Nov 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)40,8685
Polymers40,0461
Non-polymers8234
Water6,593366
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)163,47320
Polymers160,1824
Non-polymers3,29116
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 area17970 Å2
ΔGint-32 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.938, 137.938, 111.756
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-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 64.69 %
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: Jul 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.398→30 Å / Num. obs: 104389 / % possible obs: 99 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 32.3
Reflection shellResolution: 1.398→1.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 10392 / % possible all: 99.7

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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: 1.398→30 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24
RfactorNum. reflection% reflection
Rfree0.1838 5137 5 %
Rwork0.164 --
obs0.165 102688 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.398→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2483 0 58 368 2909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152780
X-RAY DIFFRACTIONf_angle_d1.3653816
X-RAY DIFFRACTIONf_dihedral_angle_d12.6531997
X-RAY DIFFRACTIONf_chiral_restr0.105434
X-RAY DIFFRACTIONf_plane_restr0.009509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3978-1.41370.24981580.23122498X-RAY DIFFRACTION77
1.4137-1.43040.23911400.22212816X-RAY DIFFRACTION85
1.4304-1.44780.22571600.20853022X-RAY DIFFRACTION91
1.4478-1.46610.25331630.21493177X-RAY DIFFRACTION97
1.4661-1.48540.2391850.20293248X-RAY DIFFRACTION99
1.4854-1.50580.24531720.20373298X-RAY DIFFRACTION99
1.5058-1.52730.21671560.19513341X-RAY DIFFRACTION100
1.5273-1.55010.19941980.19143276X-RAY DIFFRACTION100
1.5501-1.57430.22161710.18933338X-RAY DIFFRACTION100
1.5743-1.60010.2191760.18743303X-RAY DIFFRACTION100
1.6001-1.62770.20331750.18673321X-RAY DIFFRACTION100
1.6277-1.65730.19171670.17723325X-RAY DIFFRACTION100
1.6573-1.68910.19741640.17253298X-RAY DIFFRACTION100
1.6891-1.72360.18531890.17763313X-RAY DIFFRACTION100
1.7236-1.76110.19911770.17683325X-RAY DIFFRACTION100
1.7611-1.80210.16811740.17383305X-RAY DIFFRACTION100
1.8021-1.84710.16911980.17263321X-RAY DIFFRACTION100
1.8471-1.8970.20121660.16383316X-RAY DIFFRACTION100
1.897-1.95280.17621790.16883294X-RAY DIFFRACTION99
1.9528-2.01590.18731780.16143308X-RAY DIFFRACTION99
2.0159-2.08790.15981540.15963322X-RAY DIFFRACTION99
2.0879-2.17140.17861730.15653287X-RAY DIFFRACTION98
2.1714-2.27020.1631580.15893281X-RAY DIFFRACTION98
2.2702-2.38980.18211680.15723295X-RAY DIFFRACTION98
2.3898-2.53950.2021850.16513266X-RAY DIFFRACTION98
2.5395-2.73530.17531570.15683303X-RAY DIFFRACTION98
2.7353-3.01030.17391880.16223281X-RAY DIFFRACTION97
3.0103-3.44510.18181620.14983321X-RAY DIFFRACTION97
3.4451-4.33740.15811830.13663356X-RAY DIFFRACTION98
4.3374-26.69430.1781630.15823396X-RAY DIFFRACTION94

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