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- PDB-3krz: Crystal Structure of the Thermostable NADH4-bound old yellow enzy... -

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Basic information

Entry
Database: PDB / ID: 3krz
TitleCrystal Structure of the Thermostable NADH4-bound old yellow enzyme from Thermoanaerobacter pseudethanolicus E39
ComponentsNADH:flavin oxidoreductase/NADH oxidase
KeywordsOXIDOREDUCTASE / homotetramer / dimer of dimers / Tim barrel / thermophilic / old yellow enzyme / ene-reductase activity
Function / homology
Function and homology information


NADPH dehydrogenase activity / FMN binding / NADP binding
Similarity search - Function
NADPH dehydrogenase YqjM-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 / Chem-TXD / NADH:flavin oxidoreductase/NADH oxidase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus ATCC 33223 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsAdalbjornsson, B.V. / Toogood, H.S. / Leys, D. / Scrutton, N.S.
CitationJournal: Chembiochem / Year: 2010
Title: Biocatalysis with thermostable enzymes: structure and properties of a thermophilic 'ene'-reductase related to old yellow enzyme.
Authors: Adalbjornsson, B.V. / Toogood, H.S. / Fryszkowska, A. / Pudney, C.R. / Jowitt, T.A. / Leys, D. / Scrutton, N.S.
History
DepositionNov 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NADH:flavin oxidoreductase/NADH oxidase
B: NADH:flavin oxidoreductase/NADH oxidase
C: NADH:flavin oxidoreductase/NADH oxidase
D: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,40312
Polymers152,9084
Non-polymers4,4958
Water30,4451690
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7320 Å2
ΔGint-34 kcal/mol
Surface area46660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.380, 98.556, 95.134
Angle α, β, γ (deg.)90.00, 92.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NADH:flavin oxidoreductase/NADH oxidase


Mass: 38227.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter pseudethanolicus ATCC 33223 (bacteria)
Strain: 39E / Gene: Teth39_0012, ZP_00777979 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express(DE3) / References: UniProt: B0KAH1
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-TXD / 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE


Mass: 667.457 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H31N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1690 / 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: 2.68 Å3/Da / Density % sol: 54.05 % / Mosaicity: 0.177 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 50mM Magnesium formate, pH 7.0, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.501→97.59 Å / Num. obs: 229398 / % possible obs: 91.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.581.30.3951.928024209310.39557.9
1.58-1.682.60.3542.181747314750.35491
1.68-1.792.80.25390850323550.2599.8
1.79-1.942.80.1614.684923301740.16199.7
1.94-2.122.80.0997.378043276780.09999.5
2.12-2.372.80.079.870488249760.0799.2
2.37-2.742.80.0629.561647218940.06298.7
2.74-3.352.80.04911.951141183340.04997.6
3.35-4.742.80.03814.438639138910.03895.6
4.74-65.2330.03416.82296576900.03495.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.69 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.15458 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.896 / SU B: 2.076 / SU ML: 0.066 / SU R Cruickshank DPI: 0.107 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19397 7379 5 %RANDOM
Rwork0.15654 ---
obs0.157 139844 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.43 Å2 / Biso mean: 15.302 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10511 0 277 1690 12478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211261
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.98915334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46751406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04224.269499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46151997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5271575
X-RAY DIFFRACTIONr_chiral_restr0.0930.21696
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028407
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.25568
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.27771
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.21382
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.248
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9021.57024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.263210993
X-RAY DIFFRACTIONr_scbond_it2.1934947
X-RAY DIFFRACTIONr_scangle_it3.5244.54311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.218 540 -
Rwork0.185 10312 -
all-10852 -
obs--99.24 %

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