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- PDB-3p8j: Y351S mutant of pentaerythritol tetranitrate reductase containing... -

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Basic information

Entry
Database: PDB / ID: 3p8j
TitleY351S 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 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)39,9743
Polymers39,4591
Non-polymers5152
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.490, 70.309, 88.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 39459.105 Da / Num. of mol.: 1 / Mutation: Y351S
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.: 768 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
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→29.99 Å / Num. obs: 181871 / % possible obs: 93.6 % / Redundancy: 3.62 % / Rmerge(I) obs: 0.051 / Χ2: 0.99 / Net I/σ(I): 14.9 / Scaling rejects: 4973
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1-1.041.820.1923.929817163991.2985.4
1.04-1.082.650.1595.350259188611.1497.9
1.08-1.133.750.1267.772352190931.1399
1.13-1.193.810.0931073257189831.0598.6
1.19-1.263.880.07612.174440189850.9898.2
1.26-1.363.950.06414.475331189070.9397.7
1.36-1.494.020.05516.776178188160.8896.9
1.49-1.714.080.05317.676626186530.8995.8
1.71-2.154.110.04123.776033184090.9294
2.15-29.993.950.03630.95863214765173.5

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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→17.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1476 / WRfactor Rwork: 0.1343 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9323 / SU B: 0.494 / SU ML: 0.012 / SU R Cruickshank DPI: 0.0227 / SU Rfree: 0.0224 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1476 9174 5 %RANDOM
Rwork0.1341 ---
obs0.1347 181855 93.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.84 Å2 / Biso mean: 9.8627 Å2 / Biso min: 3.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1→17.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2759 0 35 768 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223003
X-RAY DIFFRACTIONr_bond_other_d0.0040.022023
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9784121
X-RAY DIFFRACTIONr_angle_other_deg0.9334954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15924.178146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15615484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8991525
X-RAY DIFFRACTIONr_chiral_restr0.1210.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023459
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02599
X-RAY DIFFRACTIONr_nbd_refined0.5170.2669
X-RAY DIFFRACTIONr_nbd_other0.2590.22467
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21483
X-RAY DIFFRACTIONr_nbtor_other0.1120.21464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2521
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2950.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.266
X-RAY DIFFRACTIONr_mcbond_it0.9141.51994
X-RAY DIFFRACTIONr_mcbond_other0.321.5760
X-RAY DIFFRACTIONr_mcangle_it1.2323012
X-RAY DIFFRACTIONr_scbond_it1.64131289
X-RAY DIFFRACTIONr_scangle_it2.2344.51086
X-RAY DIFFRACTIONr_rigid_bond_restr0.73835660
X-RAY DIFFRACTIONr_sphericity_free3.5893768
X-RAY DIFFRACTIONr_sphericity_bonded1.92334945
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 565 -
Rwork0.254 11194 -
all-11759 -
obs--82.9 %

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