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- PDB-3p7y: Pentaerythritol tetranitrate reductase co-crystal structure with ... -

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Basic information

Entry
Database: PDB / ID: 3p7y
TitlePentaerythritol tetranitrate reductase co-crystal structure with bound (E)-1-(2'-hydroxyphenyl)-2-nitroethene
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
FLAVIN MONONUCLEOTIDE / 2-[(E)-2-nitroethenyl]phenol / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsToogood, H.S. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2011
Title: A Site-Saturated Mutagenesis Study of Pentaerythritol Tetranitrate Reductase Reveals that Residues 181 and 184 Influence Ligand Binding, Stereochemistry and Reactivity.
Authors: Toogood, H.S. / Fryszkowska, A. / Hulley, M. / Sakuma, M. / Mansell, D. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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_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
A: Pentaerythritol tetranitrate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1573
Polymers39,5351
Non-polymers6212
Water13,421745
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.533, 70.349, 88.948
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: 39535.199 Da / Num. of mol.: 1
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-P7Y / 2-[(E)-2-nitroethenyl]phenol / (E)-1-(2'-hydroxyphenyl)-2-nitroethene


Mass: 165.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / 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: 45.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.2
Details: 100mM sodium cacodylate, 100 mM sodium acetate, 16-18% isopropanol, pH 6.2, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 22, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.2→55.216 Å / Num. all: 112611 / Num. obs: 112611 / % possible obs: 99.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.264.50.2742.673943163250.274100
1.26-1.344.60.2213.371012155180.221100
1.34-1.434.60.1774.167001145900.177100
1.43-1.554.60.138562226136050.138100
1.55-1.74.50.1155.856352125310.11599.9
1.7-1.94.40.1056.149666113860.10599.9
1.9-2.194.10.0877.140737100420.08799.8
2.19-2.683.60.0679.43069784670.06798.8
2.68-3.794.10.0649.82748866660.06499.1
3.79-39.8093.60.0768.11248534810.07690.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H50

1h50


Resolution: 1.2→30.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.146 / WRfactor Rwork: 0.1232 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9462 / SU B: 0.825 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0341 / SU Rfree: 0.0334 / 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
Rfree0.1475 5645 5 %RANDOM
Rwork0.1248 ---
obs0.126 112529 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.48 Å2 / Biso mean: 9.8403 Å2 / Biso min: 2.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 0 43 745 3553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223009
X-RAY DIFFRACTIONr_bond_other_d0.0020.022031
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9814124
X-RAY DIFFRACTIONr_angle_other_deg0.94434954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88923.931145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86515481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5921526
X-RAY DIFFRACTIONr_chiral_restr0.080.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_nbd_refined0.2120.2571
X-RAY DIFFRACTIONr_nbd_other0.2090.22377
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21487
X-RAY DIFFRACTIONr_nbtor_other0.0840.21513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2473
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.265
X-RAY DIFFRACTIONr_mcbond_it0.9891.51989
X-RAY DIFFRACTIONr_mcbond_other0.3621.5759
X-RAY DIFFRACTIONr_mcangle_it1.28622998
X-RAY DIFFRACTIONr_scbond_it1.82131252
X-RAY DIFFRACTIONr_scangle_it2.4484.51106
X-RAY DIFFRACTIONr_rigid_bond_restr0.84935618
X-RAY DIFFRACTIONr_sphericity_free4.0543746
X-RAY DIFFRACTIONr_sphericity_bonded1.78634960
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 417 -
Rwork0.135 7845 -
all-8262 -
obs--99.95 %

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