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- PDB-2abb: Structure of PETN reductase Y186F in complex with cyanide -

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Basic information

Entry
Database: PDB / ID: 2abb
TitleStructure of PETN reductase Y186F in complex with cyanide
Componentspentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / PETN reductase / proton transfer / flavoenzyme
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 / THIOCYANATE ION / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKhan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S.
CitationJournal: Febs J. / Year: 2005
Title: Proton transfer in the oxidative half-reaction of pentaerythritol tetranitrate reductase
Authors: Khan, H. / Barna, T. / Bruce, N.C. / Munro, A.W. / Leys, D. / Scrutton, N.S.
History
DepositionJul 15, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Non-polymer description
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9634
Polymers39,3881
Non-polymers5753
Water11,818656
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.618, 68.664, 88.602
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 / PETN reductase


Mass: 39388.000 Da / Num. of mol.: 1 / Mutation: Y186F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P71278, EC: 1.7.99.-
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


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


Mass: 18.015 Da / Num. of mol.: 656 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 43.71 %
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: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 18, 2003
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→15 Å / Num. all: 172733 / Num. obs: 169624 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 1→1.03 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.489 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VYR

1vyr


Resolution: 1→14.37 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.696 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15486 8938 5 %RANDOM
Rwork0.1384 ---
all0.13924 172733 --
obs0.13924 169624 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.713 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--0.82 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1→14.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2716 0 38 656 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212910
X-RAY DIFFRACTIONr_bond_other_d0.0030.022666
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9673981
X-RAY DIFFRACTIONr_angle_other_deg1.236188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8095370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.70523.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815450
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1151525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023283
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02578
X-RAY DIFFRACTIONr_nbd_refined0.2540.2641
X-RAY DIFFRACTIONr_nbd_other0.2590.23305
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2520
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4760.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.289
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0041.51828
X-RAY DIFFRACTIONr_mcbond_other0.4961.5747
X-RAY DIFFRACTIONr_mcangle_it1.50122942
X-RAY DIFFRACTIONr_scbond_it1.88231099
X-RAY DIFFRACTIONr_scangle_it2.7524.51033
X-RAY DIFFRACTIONr_rigid_bond_restr0.93435602
X-RAY DIFFRACTIONr_sphericity_free4.3923656
X-RAY DIFFRACTIONr_sphericity_bonded2.87835508
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 539
Rwork0.337 10677

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