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- PDB-6a39: The crystal structure of Mandelate oxidase Y128F with C4a-Malic a... -

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Basic information

Entry
Database: PDB / ID: 6a39
TitleThe crystal structure of Mandelate oxidase Y128F with C4a-Malic acid-monooxide-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-B8C / 4-hydroxymandelate oxidase
Similarity search - Component
Biological speciesAmycolatopsis orientalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsLi, T.L. / Lin, K.H.
CitationJournal: To Be Published
Title: The crystal structure of Mandelate oxidase mutant Y128F with C4a-Malic acid-monooxide-FMN adduct
Authors: Li, T.L. / Lin, K.H.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 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)40,6342
Polymers40,0301
Non-polymers6041
Water4,756264
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)162,5368
Polymers160,1184
Non-polymers2,4184
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 area9300 Å2
ΔGint-76 kcal/mol
Surface area44800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.440, 138.440, 109.144
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: 40029.562 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-B8C / (~{E})-2-[[(4~{a}~{S})-7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2~{S},3~{S},4~{S})-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-5~{H}-benzo[g]pteridin-4~{a}-yl]oxy]-3-oxidanyl-but-2-enedioic acid


Mass: 604.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C21H25N4O15P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.45 Å3/Da / Density % sol: 64.38 %
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 / 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: 1.894→30 Å / Num. obs: 40612 / % possible obs: 98.9 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.019 / Net I/σ(I): 2.62
Reflection shellResolution: 1.894→1.97 Å / Rmerge(I) obs: 0.745 / Num. unique obs: 4154 / CC1/2: 0.873 / Rpim(I) all: 0.275

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SGZ

3sgz


Resolution: 1.89→29.24 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.021 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2113 5.2 %RANDOM
Rwork0.18951 ---
obs0.19184 38499 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å2-0 Å2
2---0.09 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.89→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 42 264 2764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0132547
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172448
X-RAY DIFFRACTIONr_angle_refined_deg2.4831.6533467
X-RAY DIFFRACTIONr_angle_other_deg1.6641.5865601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5125330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.64719.635137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31315396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5871530
X-RAY DIFFRACTIONr_chiral_restr0.3280.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.022918
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02574
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_it4.2492.5041320
X-RAY DIFFRACTIONr_mcbond_other4.252.5011319
X-RAY DIFFRACTIONr_mcangle_it5.5073.7221647
X-RAY DIFFRACTIONr_mcangle_other5.5073.7251648
X-RAY DIFFRACTIONr_scbond_it5.6453.2331226
X-RAY DIFFRACTIONr_scbond_other5.6463.2331225
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9224.611820
X-RAY DIFFRACTIONr_long_range_B_refined10.26732.8443093
X-RAY DIFFRACTIONr_long_range_B_other10.26532.8413094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.894→1.943 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 130 -
Rwork0.279 2266 -
obs--77.84 %

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