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- PDB-6a24: The crystal structure of Mandelate oxidase with 3-fluoropyruvate -

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Basic information

Entry
Database: PDB / ID: 6a24
TitleThe crystal structure of Mandelate oxidase with 3-fluoropyruvate
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
FLUORIDE ION / FLAVIN MONONUCLEOTIDE / PYRUVIC ACID / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 8, 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 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_close_contact
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)40,6094
Polymers40,0461
Non-polymers5633
Water6,233346
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)162,43616
Polymers160,1824
Non-polymers2,25412
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-63 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.096, 138.096, 111.203
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 / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: Jul 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→30 Å / Num. obs: 106950 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 41.2
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10574 / % 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: 1.39→28.09 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.55
RfactorNum. reflection% reflection
Rfree0.1927 5125 4.98 %
Rwork0.1787 --
obs0.1794 102876 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.39→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 38 347 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092804
X-RAY DIFFRACTIONf_angle_d1.2333835
X-RAY DIFFRACTIONf_dihedral_angle_d13.1161019
X-RAY DIFFRACTIONf_chiral_restr0.077444
X-RAY DIFFRACTIONf_plane_restr0.006504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3899-1.40570.2908940.24541945X-RAY DIFFRACTION58
1.4057-1.42220.26861270.23792307X-RAY DIFFRACTION69
1.4222-1.43960.24991480.23152589X-RAY DIFFRACTION78
1.4396-1.45780.27361570.23472878X-RAY DIFFRACTION86
1.4578-1.4770.231460.23213186X-RAY DIFFRACTION94
1.477-1.49720.21651450.22823326X-RAY DIFFRACTION98
1.4972-1.51860.2441650.22833358X-RAY DIFFRACTION100
1.5186-1.54120.23451550.22113397X-RAY DIFFRACTION100
1.5412-1.56530.251760.21213341X-RAY DIFFRACTION100
1.5653-1.5910.20891830.20893351X-RAY DIFFRACTION100
1.591-1.61840.21531630.20663370X-RAY DIFFRACTION100
1.6184-1.64780.21451740.20153375X-RAY DIFFRACTION100
1.6478-1.67950.23051930.19893356X-RAY DIFFRACTION100
1.6795-1.71380.22671610.19573366X-RAY DIFFRACTION100
1.7138-1.75110.21422010.19563354X-RAY DIFFRACTION100
1.7511-1.79180.20931820.18853377X-RAY DIFFRACTION100
1.7918-1.83660.17881710.19223370X-RAY DIFFRACTION100
1.8366-1.88620.19311770.18413384X-RAY DIFFRACTION100
1.8862-1.94170.20961790.1883388X-RAY DIFFRACTION100
1.9417-2.00440.18081780.18423389X-RAY DIFFRACTION100
2.0044-2.0760.20131890.18293357X-RAY DIFFRACTION100
2.076-2.15910.20861880.1743401X-RAY DIFFRACTION100
2.1591-2.25730.1951950.16853368X-RAY DIFFRACTION100
2.2573-2.37630.19721810.16973404X-RAY DIFFRACTION100
2.3763-2.52510.17541720.17963411X-RAY DIFFRACTION100
2.5251-2.71990.18621780.17293431X-RAY DIFFRACTION100
2.7199-2.99330.21251840.17593416X-RAY DIFFRACTION100
2.9933-3.42580.17991830.16313459X-RAY DIFFRACTION100
3.4258-4.31360.13771620.14643512X-RAY DIFFRACTION100
4.3136-28.09590.1742180.16163585X-RAY DIFFRACTION99

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