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- PDB-3p82: H184N mutant of pentaerythritol tetranitrate reductase containing... -

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Basic information

Entry
Database: PDB / ID: 3p82
TitleH184N mutant of pentaerythritol tetranitrate reductase containing bound acetate ion
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: 2.2 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 1.2Sep 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_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)40,0273
Polymers39,5111
Non-polymers5152
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.600, 68.899, 85.542
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: 39511.152 Da / Num. of mol.: 1 / Mutation: H184N
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.: 524 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
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: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: X8 Proteum / Detector: CCD / Date: Mar 11, 2009
RadiationMonochromator: Montel 200 Mirror optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→26.4 Å / Num. all: 28870 / Num. obs: 28870 / % possible obs: 99.9 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 17.2
Reflection shellResolution: 2.252→2.393 Å / Redundancy: 11.33 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.113 / % possible all: 99.89

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
PROTEUM PLUSPLUSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H50

1h50


Resolution: 2.2→26.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2103 / WRfactor Rwork: 0.1402 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8425 / SU B: 5.294 / SU ML: 0.136 / SU R Cruickshank DPI: 0.3013 / SU Rfree: 0.2189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 914 5 %RANDOM
Rwork0.1439 ---
obs0.1478 18118 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.4 Å2 / Biso mean: 19.1172 Å2 / Biso min: 2.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20 Å2
2--1.81 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→26.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 35 524 3316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222883
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9733933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.46423.824136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84715449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4571525
X-RAY DIFFRACTIONr_chiral_restr0.1080.2431
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022256
X-RAY DIFFRACTIONr_nbd_refined0.2140.21841
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2553
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.243
X-RAY DIFFRACTIONr_mcbond_it0.8671.51859
X-RAY DIFFRACTIONr_mcangle_it1.4422909
X-RAY DIFFRACTIONr_scbond_it2.46631178
X-RAY DIFFRACTIONr_scangle_it3.6954.51018
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 81 -
Rwork0.151 1235 -
all-1316 -
obs--100 %

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