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- PDB-6gi9: Crystal structure of pentaerythritol tetranitrate reductase (PETN... -

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Basic information

Entry
Database: PDB / ID: 6gi9
TitleCrystal structure of pentaerythritol tetranitrate reductase (PETNR) mutant I107L
ComponentsPentaerythritol tetranitrate reductase
KeywordsFLAVOPROTEIN / Mutant I107L
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 / Resolution: 1.45 Å
AuthorsLevy, C.W.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilJ020192 United Kingdom
Biotechnology and Biological Sciences Research CouncilM007065 United Kingdom
Biotechnology and Biological Sciences Research CouncilH021523 United Kingdom
CitationJournal: Acs Catalysis / Year: 2018
Title: Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes.
Authors: Iorgu, A.I. / Baxter, N.J. / Cliff, M.J. / Levy, C. / Waltho, J.P. / Hay, S. / Scrutton, N.S.
History
DepositionMay 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 17, 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)41,1563
Polymers40,6401
Non-polymers5152
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-3 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.320, 70.320, 88.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Pentaerythritol tetranitrate reductase


Mass: 40640.359 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-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: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25 % (w/v) PEG 3000, 17 % (v/v) isopropanol, 0.1 M trisodium citrate, 0.1 M cacodylic acid (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.969 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 1.45→37.54 Å / Num. obs: 63458 / % possible obs: 98.68 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0633 / Rpim(I) all: 0.0378 / Rrim(I) all: 0.074 / Net I/σ(I): 13.19
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 6292 / CC1/2: 0.728 / Rpim(I) all: 0.37 / Rrim(I) all: 0.713 / % possible all: 99.31

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABA

2aba


Resolution: 1.45→37.54 Å / SU ML: 0.1354 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.1287
RfactorNum. reflection% reflectionSelection details
Rfree0.166 3221 5.08 %Random
Rwork0.1265 ---
obs0.1285 63457 98.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.75 Å2
Refinement stepCycle: LAST / Resolution: 1.45→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 35 508 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01032956
X-RAY DIFFRACTIONf_angle_d1.18734037
X-RAY DIFFRACTIONf_chiral_restr0.0917436
X-RAY DIFFRACTIONf_plane_restr0.0092544
X-RAY DIFFRACTIONf_dihedral_angle_d17.70331100
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.28951620.22562590X-RAY DIFFRACTION99.14
1.47-1.490.22991310.20442591X-RAY DIFFRACTION99.31
1.49-1.520.23561410.18042602X-RAY DIFFRACTION99.64
1.52-1.550.23591450.17322612X-RAY DIFFRACTION99.42
1.55-1.570.2141250.17152599X-RAY DIFFRACTION99.16
1.57-1.60.20371510.15192591X-RAY DIFFRACTION98.95
1.6-1.640.22411320.14822616X-RAY DIFFRACTION99.64
1.64-1.670.18771500.12572617X-RAY DIFFRACTION99.68
1.67-1.710.18141270.12422626X-RAY DIFFRACTION99.75
1.71-1.750.16071440.11292611X-RAY DIFFRACTION99.71
1.75-1.80.18431420.11452618X-RAY DIFFRACTION99.21
1.8-1.850.16431350.11792666X-RAY DIFFRACTION99.36
1.85-1.910.19511250.11842585X-RAY DIFFRACTION99.01
1.91-1.980.17791470.11712642X-RAY DIFFRACTION99.68
1.98-2.060.16261390.11242651X-RAY DIFFRACTION99.86
2.06-2.160.16831470.11072604X-RAY DIFFRACTION99.78
2.16-2.270.14241680.10682647X-RAY DIFFRACTION99.36
2.27-2.410.14631330.10932635X-RAY DIFFRACTION98.86
2.41-2.60.16211400.11292624X-RAY DIFFRACTION98.36
2.6-2.860.15551240.1172658X-RAY DIFFRACTION98.65
2.86-3.270.14881380.12092640X-RAY DIFFRACTION98.09
3.27-4.120.14061360.11882600X-RAY DIFFRACTION94.51
4.12-37.550.14731390.14362611X-RAY DIFFRACTION91.58

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