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- PDB-3kru: Crystal Structure of the Thermostable Old Yellow Enzyme from Ther... -

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Basic information

Entry
Database: PDB / ID: 3kru
TitleCrystal Structure of the Thermostable 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
ACETATE ION / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase/NADH oxidase
Similarity search - Component
Biological speciesThermoanaerobacter pseudethanolicus ATCC 33223 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 19, 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_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: 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)158,28512
Polymers156,2244
Non-polymers2,0628
Water32,9851831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-31 kcal/mol
Surface area46150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.925, 97.376, 94.388
Angle α, β, γ (deg.)90.000, 92.340, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit is the minimal biological unit. Multiples (e.g. 2-3) of the asymmetric unit have been detected in vitro.

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Components

#1: Protein
NADH:flavin oxidoreductase/NADH oxidase


Mass: 39055.910 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, NADPH dehydrogenase
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1831 / 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: 2.55 Å3/Da / Density % sol: 51.86 % / Mosaicity: 0.483 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 0.1M Na acetate, 0.1M CaCl2, 20% isopropanol, 12% ethylene glycol, pH 4.6, 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: 1.6→94.491 Å / Num. all: 574512 / Num. obs: 204058 / % possible obs: 98.9 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.692.80.3512.184027300050.35199.9
1.69-1.792.80.247379911284300.24799.8
1.79-1.912.80.1694.475144267110.16999.8
1.91-2.072.80.1096.769902248130.10999.6
2.07-2.262.80.0769.264179227490.07699.3
2.26-2.532.80.0649.957791205080.06499
2.53-2.922.80.069.750852180110.0698.3
2.92-3.582.70.04313.541275150410.04397.1
3.58-5.062.80.03814.632648114870.03895.6
5.06-65.2330.03416.91878363030.03495

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→64.82 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.161 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.91 / SU B: 1.363 / SU ML: 0.049 / SU R Cruickshank DPI: 0.074 / SU Rfree: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 10251 5 %RANDOM
Rwork0.152 ---
obs0.153 204027 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.86 Å2 / Biso mean: 18.425 Å2 / Biso min: 6.13 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→64.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10519 0 140 1831 12490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211158
X-RAY DIFFRACTIONr_bond_other_d0.0020.027535
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.97315173
X-RAY DIFFRACTIONr_angle_other_deg0.9318456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53351415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51324.271501
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95152006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2611576
X-RAY DIFFRACTIONr_chiral_restr0.0750.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212405
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022161
X-RAY DIFFRACTIONr_nbd_refined0.2080.22389
X-RAY DIFFRACTIONr_nbd_other0.2010.28732
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25460
X-RAY DIFFRACTIONr_nbtor_other0.0830.25530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.21260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.261
X-RAY DIFFRACTIONr_mcbond_it0.8211.57404
X-RAY DIFFRACTIONr_mcbond_other0.1751.52764
X-RAY DIFFRACTIONr_mcangle_it1.107211041
X-RAY DIFFRACTIONr_scbond_it1.934843
X-RAY DIFFRACTIONr_scangle_it2.7664.54100
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 741 -
Rwork0.225 14442 -
all-15183 -
obs--99.86 %

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