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- PDB-4e2d: Structure of the old yellow enzyme from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 4e2d
TitleStructure of the old yellow enzyme from Trypanosoma cruzi
ComponentsOld Yellow Protein
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 / Dehydrogenase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 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 Protein
B: Old Yellow Protein
C: Old Yellow Protein
D: Old Yellow Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,36612
Polymers170,2294
Non-polymers2,1388
Water7,368409
1
A: Old Yellow Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0923
Polymers42,5571
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Old Yellow Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0923
Polymers42,5571
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Old Yellow Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0923
Polymers42,5571
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Old Yellow Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0923
Polymers42,5571
Non-polymers5342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.774, 118.469, 111.123
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Old Yellow Protein


Mass: 42557.129 Da / Num. of mol.: 4
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


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 1.96 Å3/Da / Density % sol: 37.35 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% (w/v) polyethylene glycol 1500, 0.3 M ammonium fluoride and 10% DMSO, 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: Mar 5, 2012
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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.911
11-h,-k,l20.089
ReflectionResolution: 1.997→40 Å / Num. all: 155841 / Num. obs: 80586 / % possible obs: 90.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.997→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.251 / % 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 4E2B

4e2b


Resolution: 1.997→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.132 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24207 4013 5 %RANDOM
Rwork0.19358 ---
all0.2014 80586 --
obs0.19599 76225 90.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.694 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.84 Å2
2---0.86 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.997→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11832 0 140 409 12381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212291
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.97916698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60951513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27923.569580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.378152020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2515100
X-RAY DIFFRACTIONr_chiral_restr0.1120.21804
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219476
LS refinement shellResolution: 1.997→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 325 -
Rwork0.214 5798 -
obs--92.87 %

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