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- PDB-5lgz: Structure of Photoreduced Pentaerythritol Tetranitrate Reductase -

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Basic information

Entry
Database: PDB / ID: 5lgz
TitleStructure of Photoreduced Pentaerythritol Tetranitrate Reductase
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / PETNR / PETN reductase / FMN / FNR / Photoreduction
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
Chem-FNR / ISOPROPYL ALCOHOL / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKwon, H. / Smith, O.M. / Moody, P.C.E.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Combining X-ray and neutron crystallography with spectroscopy.
Authors: Kwon, H. / Smith, O. / Raven, E.L. / Moody, P.C.
History
DepositionJul 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)39,8954
Polymers39,3171
Non-polymers5793
Water12,070670
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint8 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.850, 68.650, 88.930
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: 39316.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: onr / Production host: Escherichia coli (E. coli) / References: UniProt: P71278
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 25 % PEG 3000 0.1 M sodium citrate 0.1M cacodylate pH 6.2 17 % isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→21.5 Å / Num. obs: 54598 / % possible obs: 96.8 % / Redundancy: 4.1 % / Net I/σ(I): 11.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H50

1h50


Resolution: 1.5→12.492 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.43
RfactorNum. reflection% reflection
Rfree0.1814 2748 5.08 %
Rwork0.146 --
obs0.1477 54130 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→12.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 39 670 3478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163097
X-RAY DIFFRACTIONf_angle_d1.3574244
X-RAY DIFFRACTIONf_dihedral_angle_d15.2631863
X-RAY DIFFRACTIONf_chiral_restr0.099453
X-RAY DIFFRACTIONf_plane_restr0.013580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52590.21441270.18512241X-RAY DIFFRACTION85
1.5259-1.55360.21141300.17832297X-RAY DIFFRACTION87
1.5536-1.58340.19431220.16842370X-RAY DIFFRACTION89
1.5834-1.61560.21921280.15582340X-RAY DIFFRACTION89
1.6156-1.65070.20551330.15012443X-RAY DIFFRACTION92
1.6507-1.6890.19531350.14582475X-RAY DIFFRACTION94
1.689-1.73110.19311550.14292519X-RAY DIFFRACTION95
1.7311-1.77780.17961410.14972555X-RAY DIFFRACTION97
1.7778-1.830.19961380.14942557X-RAY DIFFRACTION97
1.83-1.88880.23531370.17442611X-RAY DIFFRACTION98
1.8888-1.95610.21931520.19742601X-RAY DIFFRACTION99
1.9561-2.03410.20761510.15112649X-RAY DIFFRACTION99
2.0341-2.12620.21021290.14722662X-RAY DIFFRACTION100
2.1262-2.23770.19561330.14822659X-RAY DIFFRACTION100
2.2377-2.37710.20741340.16452688X-RAY DIFFRACTION100
2.3771-2.55910.17921530.14192665X-RAY DIFFRACTION100
2.5591-2.8140.16171230.14232710X-RAY DIFFRACTION100
2.814-3.21510.14191520.13232719X-RAY DIFFRACTION100
3.2151-4.0280.14291350.1172764X-RAY DIFFRACTION100
4.028-12.49260.151400.12672857X-RAY DIFFRACTION100

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