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- PDB-3p67: T26S mutant of pentaerythritol tetranitrate reductase containing ... -

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Basic information

Entry
Database: PDB / ID: 3p67
TitleT26S 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


FMN binding / oxidoreductase activity / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsToogood, H.S. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2010
Title: Focused Directed Evolution of Pentaerythritol Tetranitrate Reductase by Using Automated Anaerobic Kinetic Screening of Site-Saturated Libraries
Authors: Hulley, M.E. / Toogood, H.S. / Fryszkowska, A. / Mansell, D. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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)41,1423
Polymers40,6261
Non-polymers5152
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.919, 69.063, 88.871
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: 40626.332 Da / Num. of mol.: 1 / Mutation: T26S
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.: 675 / 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: 2.15 Å3/Da / Density % sol: 42.78 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2008
RadiationMonochromator: Osmic blue optics - mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.5→54.554 Å / Num. all: 56705 / Num. obs: 56705 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.584.30.1880.1644.33523381610.0890.1880.1646.3100
1.58-1.684.40.1290.1146.23427177880.0610.1290.1149.8100
1.68-1.794.50.1050.0927.43246872800.0490.1050.09214100
1.79-1.944.50.0880.0788.33086768220.0410.0880.07817.7100
1.94-2.124.60.0720.0639.92887363000.0330.0720.06322.1100
2.12-2.374.60.0620.05511.22657257260.0290.0620.05524.9100
2.37-2.744.70.0610.05410.22371550620.0280.0610.05428.7100
2.74-3.354.70.0580.05110.82020743110.0260.0580.05133.999.9
3.35-4.744.70.0480.04313.41592233840.0220.0480.04336.499.5
4.74-16.4764.60.0450.0413.4858718710.020.0450.0435.796.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å16.48 Å
Translation3 Å16.48 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H50

1h50


Resolution: 1.5→16.35 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1547 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9132 / SU B: 2.12 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0895 / SU Rfree: 0.0668 / Cross valid method: THROUGHOUT / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1706 2872 5.1 %RANDOM
Rwork0.1458 ---
obs0.147 56644 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.5 Å2 / Biso mean: 14.5332 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→16.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 35 675 3466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222938
X-RAY DIFFRACTIONr_bond_other_d0.0080.021974
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9734021
X-RAY DIFFRACTIONr_angle_other_deg0.97634813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4715390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75623.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62615464
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2431526
X-RAY DIFFRACTIONr_chiral_restr0.0720.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined0.2040.2589
X-RAY DIFFRACTIONr_nbd_other0.2050.22303
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21484
X-RAY DIFFRACTIONr_nbtor_other0.0830.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2480
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.264
X-RAY DIFFRACTIONr_mcbond_it0.7751.51961
X-RAY DIFFRACTIONr_mcbond_other0.3031.5752
X-RAY DIFFRACTIONr_mcangle_it1.07622964
X-RAY DIFFRACTIONr_scbond_it1.65831192
X-RAY DIFFRACTIONr_scangle_it2.2384.51042
X-RAY DIFFRACTIONr_rigid_bond_restr0.89735473
X-RAY DIFFRACTIONr_sphericity_free3.2623675
X-RAY DIFFRACTIONr_sphericity_bonded1.38534839
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 198 -
Rwork0.235 3916 -
all-4114 -
obs--99.98 %

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