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- PDB-4e2b: High resolution crystal structure of the old yellow enzyme from T... -

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Basic information

Entry
Database: PDB / ID: 4e2b
TitleHigh resolution crystal structure of the old yellow enzyme from Trypanosoma cruzi
ComponentsOld Yellow EnzymeNADPH dehydrogenase
KeywordsOXIDOREDUCTASE / TIM-barrel fold
Function / homology
Function and homology information


FMN binding / oxidoreductase activity / cytoplasm
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 / DI(HYDROXYETHYL)ETHER / Dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.269 Å
AuthorsMurakami, M.T. / Rodrigues, N.C. / Gava, L.M. / Canduri, F. / Oliva, G. / Barbosa, L.R.S. / Borgers, J.C.
CitationJournal: To be Published
Title: High resolution crystal structure and in solution studies of the old yellow enzyme from Trypanosoma cruzi: Insights into oligomerization, enzyme dynamics and specificity
Authors: Murakami, M.T. / Rodrigues, N.C. / Gava, L.M. / Canduri, F. / Oliva, G. / Barbosa, L.R.S. / Borgers, J.C.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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: Old Yellow Enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6088
Polymers42,5571
Non-polymers1,0517
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.347, 68.656, 85.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Old Yellow Enzyme / NADPH dehydrogenase


Mass: 42557.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2TJB8
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.97 Å3/Da / Density % sol: 37.57 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% (w/v) polyethylene glycol 1500 and 0.3 M ammonium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.46 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.46 Å / Relative weight: 1
ReflectionResolution: 1.269→30 Å / Num. all: 105031 / Num. obs: 87922 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.047
Reflection shellResolution: 1.269→1.32 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.522 / % possible all: 99.9

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Processing

Software
NameVersionClassification
NatXraydata collection
MOLREPphasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ATY

3aty


Resolution: 1.269→22.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.96 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.01 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17084 4409 5 %RANDOM
Rwork0.14592 ---
obs0.14718 83454 98.3 %-
all-87922 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.677 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å2-0 Å2-0 Å2
2---0.25 Å20 Å2
3---1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.269→22.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 70 363 3398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023179
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9874321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8795403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74923.537147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.61315530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4421526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212433
X-RAY DIFFRACTIONr_rigid_bond_restr1.78433179
X-RAY DIFFRACTIONr_sphericity_free11.695595
X-RAY DIFFRACTIONr_sphericity_bonded6.72653371
LS refinement shellResolution: 1.269→1.302 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 352 -
Rwork0.186 6096 -
obs--98.76 %

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