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- PDB-3p74: H181N mutant of pentaerythritol tetranitrate reductase containing... -

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Basic information

Entry
Database: PDB / ID: 3p74
TitleH181N mutant of pentaerythritol tetranitrate reductase containing a C-terminal His8-tag
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 / Pentaerythritol tetranitrate reductase
Similarity search - Component
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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)41,0732
Polymers40,6161
Non-polymers4561
Water11,259625
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.119, 69.086, 88.623
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: 40616.312 Da / Num. of mol.: 1 / Mutation: H181N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 2.23 Å3/Da / Density % sol: 44.79 %
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: Dec 4, 2008
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→54.486 Å / Num. all: 111751 / Num. obs: 111751 / % possible obs: 98.3 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.2-1.263.40.2442.550757149550.24491.4
1.26-1.345.30.2193.382255155450.21999.8
1.34-1.435.90.1554.886013146460.155100
1.43-1.555.90.0997.380682136910.099100
1.55-1.75.90.06311.274424126180.063100
1.7-1.95.90.0513.167501114530.0599.9
1.9-2.195.80.0589.859025101110.05899.9
2.19-2.685.70.05111.34933386390.05199.9
2.68-3.795.30.02921.43552766800.02999
3.79-49.2075.10.025231741034130.02588.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å44.31 Å
Translation3 Å44.31 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→44.32 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.166 / WRfactor Rwork: 0.1417 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9329 / SU B: 0.928 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0361 / SU Rfree: 0.0354 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1587 5582 5 %RANDOM
Rwork0.1359 ---
obs0.137 111664 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.74 Å2 / Biso mean: 13.9864 Å2 / Biso min: 4.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.2→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 31 625 3406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222948
X-RAY DIFFRACTIONr_bond_other_d0.0020.021968
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.9684045
X-RAY DIFFRACTIONr_angle_other_deg0.92634803
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7055397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06723.714140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11715458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3131526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02603
X-RAY DIFFRACTIONr_nbd_refined0.2090.2555
X-RAY DIFFRACTIONr_nbd_other0.210.22202
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21460
X-RAY DIFFRACTIONr_nbtor_other0.0860.21448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2366
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0730.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3530.249
X-RAY DIFFRACTIONr_mcbond_it1.1061.51978
X-RAY DIFFRACTIONr_mcbond_other0.5791.5757
X-RAY DIFFRACTIONr_mcangle_it1.49222985
X-RAY DIFFRACTIONr_scbond_it2.05431192
X-RAY DIFFRACTIONr_scangle_it2.7174.51042
X-RAY DIFFRACTIONr_rigid_bond_restr1.03135484
X-RAY DIFFRACTIONr_sphericity_free5.2123625
X-RAY DIFFRACTIONr_sphericity_bonded3.03934838
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 326 -
Rwork0.191 6852 -
all-7178 -
obs--86.22 %

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