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- PDB-6ai7: Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct -

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Basic information

Entry
Database: PDB / ID: 6ai7
TitleMandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct
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-9Q6 / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: To Be Published
Title: The crystal structure of Mandelate oxidase mutant-Y128F with the C4a-OH-FMN adduct
Authors: Li, T.L. / Lin, K.H.
History
DepositionAug 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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)38,6152
Polymers38,1401
Non-polymers4741
Water1,33374
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)154,4598
Polymers152,5624
Non-polymers1,8974
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 area9580 Å2
ΔGint-73 kcal/mol
Surface area44860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.576, 138.576, 107.889
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: 38140.473 Da / Num. of mol.: 1 / Mutation: y128f
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-9Q6 / 1-deoxy-1-[(4aS)-4a-hydroxy-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol


Mass: 474.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.4 Å3/Da / Density % sol: 63.77 %
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 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→30 Å / Num. obs: 32246 / % possible obs: 100 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Χ2: 0.924 / Net I/σ(I): 30.2
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3167 / CC1/2: 0.911 / Rpim(I) all: 0.22 / Χ2: 0.809 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 2.07→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.903 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.157 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24618 1561 5 %RANDOM
Rwork0.20475 ---
obs0.20681 29522 96.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.796 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.29 Å2
Refinement stepCycle: 1 / Resolution: 2.07→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 32 74 2558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0192634
X-RAY DIFFRACTIONr_bond_other_d0.0040.022571
X-RAY DIFFRACTIONr_angle_refined_deg2.1161.9823605
X-RAY DIFFRACTIONr_angle_other_deg1.1463.0025881
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15622.321112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.61415420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5221532
X-RAY DIFFRACTIONr_chiral_restr0.1250.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213050
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02596
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1893.1141361
X-RAY DIFFRACTIONr_mcbond_other3.1873.111360
X-RAY DIFFRACTIONr_mcangle_it4.5944.6291711
X-RAY DIFFRACTIONr_mcangle_other4.5934.6331712
X-RAY DIFFRACTIONr_scbond_it3.7063.7081272
X-RAY DIFFRACTIONr_scbond_other3.7013.7071271
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7275.391886
X-RAY DIFFRACTIONr_long_range_B_refined8.7530.15511339
X-RAY DIFFRACTIONr_long_range_B_other8.74830.1711309
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.068→2.122 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 78 -
Rwork0.237 1642 -
obs--73.66 %

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