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- PDB-6bka: Crystal Structure of Nitronate Monooxygenase from Cyberlindnera s... -

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Basic information

Entry
Database: PDB / ID: 6bka
TitleCrystal Structure of Nitronate Monooxygenase from Cyberlindnera saturnus
ComponentsNitronate monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase / Propionate 3-nitronate
Function / homologynitronate monooxygenase / nitronate monooxygenase activity / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel / Chem-33O / FLAVIN MONONUCLEOTIDE / Nitronate monooxygenase
Function and homology information
Biological speciesCyberlindnera mrakii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAgniswamy, J. / Fang, Y.-F. / Weber, I.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1506518 United States
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of yeast nitronate monooxygenase from Cyberlindnera saturnus.
Authors: Agniswamy, J. / Reis, R.A.G. / Wang, Y.F. / Smitherman, C. / Su, D. / Weber, I. / Gadda, G.
History
DepositionNov 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitronate monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6854
Polymers41,5461
Non-polymers1,1393
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-6 kcal/mol
Surface area15830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.820, 68.430, 58.366
Angle α, β, γ (deg.)90.00, 106.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitronate monooxygenase / 2-nitropropane dioxygenase / 2-NPD / Nitroalkane oxidase


Mass: 41545.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyberlindnera mrakii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q12723, nitronate monooxygenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-33O / 3,6,9,12,15,18,21,24,27,30,33,36-dodecaoxaoctatriacontane-1,38-diol / Tridecaethyleneglycol


Mass: 590.699 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H54O14
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 21% PEG 3350, 70 mM Sodium Citrate at pH 4.0 and 100 mM Ammonium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 39464 / % possible obs: 96 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.037 / Net I/σ(I): 18.3
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2967 / CC1/2: 0.782 / Χ2: 1.08 / % possible all: 72.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q4K

4q4k


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.808 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17899 1989 5 %RANDOM
Rwork0.13982 ---
obs0.14173 37455 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å2-0.01 Å2
2---0.19 Å2-0 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 71 273 3272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193262
X-RAY DIFFRACTIONr_bond_other_d0.0060.023122
X-RAY DIFFRACTIONr_angle_refined_deg2.0891.9884442
X-RAY DIFFRACTIONr_angle_other_deg1.12937265
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7225.035141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94315572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7231514
X-RAY DIFFRACTIONr_chiral_restr0.1540.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213697
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02713
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_it1.9061.6121589
X-RAY DIFFRACTIONr_mcbond_other1.9021.6111588
X-RAY DIFFRACTIONr_mcangle_it2.6822.422010
X-RAY DIFFRACTIONr_mcangle_other2.6822.4222011
X-RAY DIFFRACTIONr_scbond_it2.9311.9631673
X-RAY DIFFRACTIONr_scbond_other2.9311.9631673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5322.792420
X-RAY DIFFRACTIONr_long_range_B_refined5.90813.8883967
X-RAY DIFFRACTIONr_long_range_B_other5.83913.6123866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.643→1.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 96 -
Rwork0.245 1896 -
obs--65.81 %

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