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- PDB-3p62: Wild-type pentaerythritol tetranitrate reductase containing a C-t... -

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Basic information

Entry
Database: PDB / ID: 3p62
TitleWild-type pentaerythritol tetranitrate reductase containing a C-terminal 8-histidine tag
ComponentsPentaerythritol tetranitrate reductase
KeywordsOXIDOREDUCTASE / old yellow enzyme family / alpha / beta barrel / Alkene reduction
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsToogood, H.S. / Hulley, M.E. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2010
Title: Focused Directed Evolution of Pentaerythritol Tetranitrate Reductase by Using Automated Anaerobic Kinetic Screening of Site-Saturated Libraries
Authors: Hulley, M.E. / Toogood, H.S. / Fryszkowska, A. / Mansell, D. / Stephens, G.M. / Gardiner, J.M. / Scrutton, N.S.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)41,1563
Polymers40,6401
Non-polymers5152
Water12,574698
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.961, 68.954, 88.476
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: 40640.359 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-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.: 698 / 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: 44.41 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Sep 1, 2009
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: 1.4→54.393 Å / Num. all: 71252 / Num. obs: 71252 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.4-1.483.40.3450.292.535528103570.1840.3450.293.899.9
1.48-1.573.40.2340.1973.73370197910.1240.2340.1975.4100
1.57-1.673.40.1750.1484.83168791890.0920.1750.1487.499.9
1.67-1.813.40.1410.1195.82965086030.0740.1410.1199.799.9
1.81-1.983.40.1050.0897.32698779400.0550.1050.08912.699.9
1.98-2.213.30.0760.064102346571510.040.0760.06416.199.5
2.21-2.563.40.0710.06102129762890.0370.0710.0619.998.7
2.56-3.133.70.0620.053111994654270.0310.0620.05325.999.6
3.13-4.433.60.0570.04912.41512441780.0290.0570.04927.998.7
4.43-37.2423.40.0540.04513800623270.0280.0540.04527.295.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.21data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H50

1h50


Resolution: 1.4→27.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.1673 / WRfactor Rwork: 0.1351 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9335 / SU B: 1.608 / SU ML: 0.029 / SU R Cruickshank DPI: 0.0569 / SU Rfree: 0.0511 / Cross valid method: THROUGHOUT / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1559 3605 5.1 %RANDOM
Rwork0.1258 ---
obs0.1273 71195 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.63 Å2 / Biso mean: 14.9066 Å2 / Biso min: 3.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 35 698 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222939
X-RAY DIFFRACTIONr_bond_other_d0.0020.021969
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9694016
X-RAY DIFFRACTIONr_angle_other_deg0.94934797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.29823.83141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.11115461
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681525
X-RAY DIFFRACTIONr_chiral_restr0.0860.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023373
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02595
X-RAY DIFFRACTIONr_nbd_refined0.2170.2575
X-RAY DIFFRACTIONr_nbd_other0.2180.22258
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21466
X-RAY DIFFRACTIONr_nbtor_other0.0860.21518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2477
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.264
X-RAY DIFFRACTIONr_mcbond_it1.3031.51966
X-RAY DIFFRACTIONr_mcbond_other0.5781.5752
X-RAY DIFFRACTIONr_mcangle_it1.67822954
X-RAY DIFFRACTIONr_scbond_it2.45731198
X-RAY DIFFRACTIONr_scangle_it3.2934.51051
X-RAY DIFFRACTIONr_rigid_bond_restr1.20935479
X-RAY DIFFRACTIONr_sphericity_free5.9913698
X-RAY DIFFRACTIONr_sphericity_bonded2.69834837
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 275 -
Rwork0.162 4969 -
all-5244 -
obs--99.85 %

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