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- PDB-6s32: Crystal structure of ene-reductase CtOYE from Chroococcidiopsis t... -

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Basic information

Entry
Database: PDB / ID: 6s32
TitleCrystal structure of ene-reductase CtOYE from Chroococcidiopsis thermalis.
ComponentsNADH:flavin oxidoreductase/NADH oxidase
KeywordsFLAVOPROTEIN / ene-reductase / Old Yellow Enzyme / Biocatalysis
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
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
ACETATE ION / BENZAMIDINE / FLAVIN MONONUCLEOTIDE / NADH:flavin oxidoreductase/NADH oxidase
Similarity search - Component
Biological speciesChroococcidiopsis thermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsRobescu, M.R. / Niero, M. / Hall, M. / Bergantino, E. / Cendron, L.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2020
Title: Two new ene-reductases from photosynthetic extremophiles enlarge the panel of old yellow enzymes: CtOYE and GsOYE.
Authors: Robescu, M.S. / Niero, M. / Hall, M. / Cendron, L. / Bergantino, E.
History
DepositionJun 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / refine / refine_hist / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)172,69513
Polymers170,5134
Non-polymers2,1829
Water25,0771392
1
A: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2644
Polymers42,6281
Non-polymers6363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1443
Polymers42,6281
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1443
Polymers42,6281
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1443
Polymers42,6281
Non-polymers5152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.658, 78.172, 108.685
Angle α, β, γ (deg.)104.23, 99.98, 90.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NADH:flavin oxidoreductase/NADH oxidase


Mass: 42628.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chroococcidiopsis thermalis (bacteria) / Gene: Chro_0590 / Production host: Escherichia coli (E. coli) / References: UniProt: K9TVC9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.85 M sodium citrate tribasic dihydrate, 0.1 M Tris pH 8.0, 0.1 M NaCl, 0.10 mM Fos-Choline 12

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.35→48.86 Å / Num. obs: 312849 / % possible obs: 90.89 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 5.76
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.535 / Mean I/σ(I) obs: 1.63 / Num. unique obs: 29361 / % possible all: 85.78

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GWJ

1gwj


Resolution: 1.35→48.86 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 3.004 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25466 15465 5 %RANDOM
Rwork0.20563 ---
obs0.20807 295972 90.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.791 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20.36 Å20.44 Å2
2---0.47 Å20.33 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10865 0 149 1392 12406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01211338
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0081.65515447
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7351409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77121.42634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.545151712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6771593
X-RAY DIFFRACTIONr_chiral_restr0.1320.21398
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.029034
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4341.6125640
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.772.4227045
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3071.8235698
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.66723.54718781
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.503311338
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 1066 -
Rwork0.267 20764 -
obs--86.03 %

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