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- PDB-3f03: Crystal structure of Pentaerythritol Tetranitrate Reductase compl... -

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Basic information

Entry
Database: PDB / ID: 3f03
TitleCrystal structure of Pentaerythritol Tetranitrate Reductase complex with 1-nitrocyclohexene
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / Asymmetric hydrogenatio / bioreduction / biocatalysis / nitroalkenes / pentaerythritol tetranitrate reductase / stereo-control
Function / homology
Function and homology information


NADPH dehydrogenase activity / 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
FLAVIN MONONUCLEOTIDE / ISOPROPYL ALCOHOL / 1-nitrocyclohexene / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 Å
AuthorsRoujeinikova, A.R. / Toogood, H.S. / Leys, D.
CitationJournal: To be published
Title: Structure-based insight into the asymmetric bioreduction of the C=C double bond of alpha,beta-unsaturated nitroalkenes by pentaerythritol tetranitrate reductase.
Authors: Toogood, H.S. / Fryszkowska, A. / Hare, V. / Fisher, K. / Roujeinikova, A. / Leys, D. / Gardiner, J.M. / Stephens, G.M. / Scrutton, N.S.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
K: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0835
Polymers39,4041
Non-polymers6794
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.338, 70.295, 89.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules K

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 39404.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Strain: PB2 / Gene: onr / Plasmid: pONR1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P71278, EC: 1.7.99.-

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Non-polymers , 5 types, 657 molecules

#2: Chemical ChemComp-NYH / 1-nitrocyclohexene


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsNYH AND IPA ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 25 % (w/v) PEG 3000, 0.1M trisodium citrate, 0.1M cacodylic acid pH 6.2, 17 % (v/v) isopropanol , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.2→44.432 Å / Num. obs: 112379 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.05
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.263.30.481.454205162240.4899.5
1.26-1.343.40.371.852299154160.3799.9
1.34-1.433.40.2752.549904145520.27599.9
1.43-1.553.40.1843.846760135660.18499.9
1.55-1.73.40.1225.642856124780.12299.9
1.7-1.93.40.0837.938843113380.08399.9
1.9-2.193.40.0659.534017100130.06599.8
2.19-2.683.20.04513.32714884590.04599.1
2.68-3.793.40.03714.62279266480.03799.4
3.79-44.433.40.03117.81254636850.03197.1

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 1.34→15 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.259 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.145 4075 5 %RANDOM
Rwork0.115 ---
obs0.116 80902 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.25 Å2 / Biso mean: 11.079 Å2 / Biso min: 3.94 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å20 Å2
2---0.44 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.34→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2867 0 50 657 3574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222981
X-RAY DIFFRACTIONr_bond_other_d0.0020.022011
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9764064
X-RAY DIFFRACTIONr_angle_other_deg1.04934903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0385369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.53324.082147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20415479
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7641526
X-RAY DIFFRACTIONr_chiral_restr0.1020.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02588
X-RAY DIFFRACTIONr_nbd_refined0.2190.2601
X-RAY DIFFRACTIONr_nbd_other0.2110.22363
X-RAY DIFFRACTIONr_nbtor_refined0.180.21484
X-RAY DIFFRACTIONr_nbtor_other0.0870.21518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2410
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.242
X-RAY DIFFRACTIONr_mcbond_it1.4421.51959
X-RAY DIFFRACTIONr_mcbond_other0.6951.5745
X-RAY DIFFRACTIONr_mcangle_it1.83222969
X-RAY DIFFRACTIONr_scbond_it2.56631270
X-RAY DIFFRACTIONr_scangle_it3.494.51095
X-RAY DIFFRACTIONr_rigid_bond_restr1.28535578
X-RAY DIFFRACTIONr_sphericity_free8.0173657
X-RAY DIFFRACTIONr_sphericity_bonded4.43134930
LS refinement shellResolution: 1.34→1.375 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 302 -
Rwork0.14 5607 -
all-5909 -
obs--99.93 %

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