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- PDB-7o0t: Crystal structure of Chloroflexus aggregans ene-reductase CaOYE h... -

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Basic information

Entry
Database: PDB / ID: 7o0t
TitleCrystal structure of Chloroflexus aggregans ene-reductase CaOYE holoenzyme
ComponentsNADH:flavin oxidoreductase/NADH oxidase
KeywordsOXIDOREDUCTASE / ene-reductase / FMN-binding protein / Old Yellow Enzyme
Function / homology
Function and homology information


NADPH dehydrogenase / 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-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / MALONATE ION / NADPH dehydrogenase
Similarity search - Component
Biological speciesChloroflexus aggregans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRobescu, M.S. / Niero, M. / Loprete, G. / Bergantino, E. / Cendron, L.
CitationJournal: Microorganisms / Year: 2021
Title: A New Thermophilic Ene-Reductase from the Filamentous Anoxygenic Phototrophic Bacterium Chloroflexus aggregans .
Authors: Robescu, M.S. / Niero, M. / Loprete, G. / Cendron, L. / Bergantino, E.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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

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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)153,50813
Polymers151,1734
Non-polymers2,3369
Water3,387188
1
A: NADH:flavin oxidoreductase/NADH oxidase
C: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7036
Polymers75,5862
Non-polymers1,1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-9 kcal/mol
Surface area23950 Å2
MethodPISA
2
B: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules

D: NADH:flavin oxidoreductase/NADH oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8057
Polymers75,5862
Non-polymers1,2195
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x+1/2,y+1/2,z1
Buried area5450 Å2
ΔGint-7 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.194, 162.274, 216.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
NADH:flavin oxidoreductase/NADH oxidase


Mass: 37793.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aggregans (strain MD-66 / DSM 9485) (bacteria)
Strain: MD-66 / DSM 9485 / Gene: Cagg_2779 / Production host: Escherichia coli (E. coli) / References: UniProt: B8G5D6
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.14 Å3/Da / Density % sol: 60.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES pH 7.0, 1.1 M sodium malonate dibasic monohydrate, 0.5% v/v Jeffamine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jun 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→38.01 Å / Num. obs: 73908 / % possible obs: 99.3 % / Redundancy: 4.6 % / CC1/2: 0.969 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.61 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4571 / CC1/2: 0.74 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nux

5nux


Resolution: 2.4→38.01 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.353 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 3677 5 %RANDOM
Rwork0.2198 ---
obs0.2219 70188 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.95 Å2 / Biso mean: 34.188 Å2 / Biso min: 9.86 Å2
Baniso -1Baniso -2Baniso -3
1--2.09 Å20 Å2-0 Å2
2--3.35 Å20 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 2.4→38.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10664 0 159 188 11011
Biso mean--26.97 29.45 -
Num. residues----1416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211209
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.63315351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61451430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54619.426575
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.601151617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.12315118
X-RAY DIFFRACTIONr_chiral_restr0.1040.21445
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028822
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 298 -
Rwork0.307 5164 -
all-5462 -
obs--99.96 %

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