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- PDB-3p8i: Y351F mutant of pentaerythritol tetranitrate reductase containing... -

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Basic information

Entry
Database: PDB / ID: 3p8i
TitleY351F mutant of pentaerythritol tetranitrate reductase containing a bound acetate molecule
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / old yellow enzyme family / alpha / beta barrel
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / FMN binding / cytosol
Similarity search - Function
Oxidoreductase Oye-like / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.19 Å
AuthorsToogood, H.S. / Scrutton, N.S.
CitationJournal: Catalysis Science and Technology / Year: 2011
Title: Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions ...Title: Active site modifications in pentaerythritol tetranitrate reductase can lead to improved product enantiopurity, decreased by-product formation and altered stereochemical outcome in reactions with a,b-unsaturated nitroolefins
Authors: Fryszkowska, A. / Toogood, H.S. / Sakuma, M. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S.
History
DepositionOct 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0353
Polymers39,5191
Non-polymers5152
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.685, 68.838, 88.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 39519.199 Da / Num. of mol.: 1 / Mutation: Y351F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr, PETNR / Plasmid: pBluescript II-KS(+) / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, NADPH dehydrogenase
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 774 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Apr 22, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.19→37.4 Å / Num. all: 111179 / Num. obs: 111179 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.6
Reflection shellResolution: 1.19→1.23 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.4 / % possible all: 99.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H50

1h50


Resolution: 1.19→7.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1452 / WRfactor Rwork: 0.1276 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.9359 / SU B: 0.936 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0352 / SU Rfree: 0.0331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1467 5564 5 %RANDOM
Rwork0.1293 ---
obs0.1302 110924 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.46 Å2 / Biso mean: 13.1949 Å2 / Biso min: 4.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.19→7.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 0 35 774 3567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222945
X-RAY DIFFRACTIONr_bond_other_d0.0020.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9724030
X-RAY DIFFRACTIONr_angle_other_deg1.37934834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.52323.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93615467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3081527
X-RAY DIFFRACTIONr_chiral_restr0.0820.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023388
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02602
X-RAY DIFFRACTIONr_nbd_refined0.2110.2564
X-RAY DIFFRACTIONr_nbd_other0.2240.22246
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21460
X-RAY DIFFRACTIONr_nbtor_other0.0770.21519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2538
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.274
X-RAY DIFFRACTIONr_mcbond_it1.2021.51978
X-RAY DIFFRACTIONr_mcbond_other0.8671.5752
X-RAY DIFFRACTIONr_mcangle_it1.54522966
X-RAY DIFFRACTIONr_scbond_it2.11831194
X-RAY DIFFRACTIONr_scangle_it3.0124.51049
X-RAY DIFFRACTIONr_rigid_bond_restr1.09535505
X-RAY DIFFRACTIONr_sphericity_free4.5713774
X-RAY DIFFRACTIONr_sphericity_bonded3.48834856
LS refinement shellResolution: 1.19→1.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 394 -
Rwork0.174 7579 -
all-7973 -
obs--99.66 %

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