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- PDB-7bsr: Mandelate oxidase with the 2-Hydroxy-3-oxosuccinic acid -

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Basic information

Entry
Database: PDB / ID: 7bsr
TitleMandelate oxidase with the 2-Hydroxy-3-oxosuccinic 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-F7C / Chem-F7F / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.894 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
DepositionMar 31, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)38,7613
Polymers38,1401
Non-polymers6202
Water2,000111
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)155,04412
Polymers152,5624
Non-polymers2,4828
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 area9120 Å2
ΔGint-71 kcal/mol
Surface area44620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.440, 138.440, 109.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein 4-hydroxymandelate oxidase


Mass: 38140.473 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-F7F / 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE


Mass: 472.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-F7C / (2~{S})-2-oxidanyl-3-oxidanylidene-butanedioic acid


Mass: 148.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.73 Å3/Da / Density % sol: 67.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 35% Tascimate, 0.1M Bis-Tris propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→30 Å / Num. obs: 41750 / % possible obs: 98.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 18.8043593687 Å2 / Rmerge(I) obs: 0.039 / Net I/av σ(I): 2.6 / Net I/σ(I): 36.4
Reflection shellResolution: 1.894→1.97 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4154 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.7refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 1.894→29.228 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2113 5.2 %RANDOM
Rwork0.2202 ---
obs0.2221 40611 96.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 146.52 Å2 / Biso mean: 28.6778 Å2 / Biso min: 6.48 Å2
Refinement stepCycle: final / Resolution: 1.894→29.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 44 111 2613
Biso mean--28.88 24.7 -
Num. residues----330
LS refinement shellResolution: 1.89→1.94 Å
RfactorNum. reflection% reflection
Rfree0.3451 --
Rwork0.3059 --
obs-2025 77.2 %

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