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- PDB-3atz: Crystal structure of TcOYE with pHBA -

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Basic information

Entry
Database: PDB / ID: 3atz
TitleCrystal structure of TcOYE with pHBA
ComponentsProstaglandin F2a synthase
KeywordsOxidoreductase/Oxidoreductase inhibitor / alpha/beta barrel / flavin mononucleotide / Oxidoreductase-Oxidoreductase inhibitor complex
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 / P-HYDROXYBENZALDEHYDE / Prostaglandin F2a synthase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsOkamoto, N. / Yamaguchi, K. / Mizohata, E. / Tokuoka, K. / Uchiyama, N. / Sugiyama, S. / Matsumura, H. / Inaka, K. / Urade, Y. / Inoue, T.
CitationJournal: J.Biochem. / Year: 2011
Title: Structural insight into the stereoselective production of PGF2(alpha) by Old Yellow Enzyme from Trypanosoma cruzi
Authors: Okamoto, N. / Yamaguchi, K. / Mizohata, E. / Tokuoka, K. / Uchiyama, N. / Sugiyama, S. / Matsumura, H. / Inaka, K. / Urade, Y. / Inoue, T.
History
DepositionJan 26, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 13, 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: Prostaglandin F2a synthase
B: Prostaglandin F2a synthase
C: Prostaglandin F2a synthase
D: Prostaglandin F2a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,56512
Polymers169,2514
Non-polymers2,3148
Water10,431579
1
A: Prostaglandin F2a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8913
Polymers42,3131
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Prostaglandin F2a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8913
Polymers42,3131
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Prostaglandin F2a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8913
Polymers42,3131
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Prostaglandin F2a synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8913
Polymers42,3131
Non-polymers5782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.333, 119.587, 111.527
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Prostaglandin F2a synthase / TcOYE


Mass: 42312.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TcPGFS / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I6L9
#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-HBA / P-HYDROXYBENZALDEHYDE


Mass: 122.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 1.86 Å3/Da / Density % sol: 34.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000, Ammonium fluoride, Urea, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jun 29, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 78333 / % possible obs: 100 % / Biso Wilson estimate: 14.5 Å2
Reflection shellResolution: 2.05→2.12 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→37.18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 319756.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3832 5 %RANDOM
Rwork0.172 ---
obs0.172 75907 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.9481 Å2 / ksol: 0.338905 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.59 Å20 Å22.13 Å2
2---4.49 Å20 Å2
3---9.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2.04→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11715 0 160 579 12454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.241.5
X-RAY DIFFRACTIONc_mcangle_it4.812
X-RAY DIFFRACTIONc_scbond_it5.962
X-RAY DIFFRACTIONc_scangle_it7.052.5
Refine LS restraints NCSNCS model details: NONE
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4p-HBA4.paramp-HBA4.top
X-RAY DIFFRACTION5FMN.paramFMN.top

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