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- PDB-4qly: Crystal structure of CLA-ER, a novel enone reductase catalyzing a... -

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Basic information

Entry
Database: PDB / ID: 4qly
TitleCrystal structure of CLA-ER, a novel enone reductase catalyzing a key step of a gut-bacterial fatty acid saturation metabolism, biohydrogenation
ComponentsEnone reductase CLA-ER
KeywordsOXIDOREDUCTASE / NADH oxidase/flavin reductase family / enone reductase / FMN
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / NADH dehydrogenase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsHou, F. / Miyakawa, T. / Tanokura, M.
CitationJournal: Febs J. / Year: 2015
Title: Structure and reaction mechanism of a novel enone reductase.
Authors: Hou, F. / Miyakawa, T. / Kitamura, N. / Takeuchi, M. / Park, S.B. / Kishino, S. / Ogawa, J. / Tanokura, M.
History
DepositionJun 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enone reductase CLA-ER
B: Enone reductase CLA-ER
C: Enone reductase CLA-ER
D: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6298
Polymers97,8034
Non-polymers1,8254
Water6,449358
1
A: Enone reductase CLA-ER
B: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8144
Polymers48,9022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8080 Å2
ΔGint-55 kcal/mol
Surface area17700 Å2
MethodPISA
2
C: Enone reductase CLA-ER
D: Enone reductase CLA-ER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8144
Polymers48,9022
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-53 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.710, 60.913, 72.561
Angle α, β, γ (deg.)85.57, 98.92, 111.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Enone reductase CLA-ER


Mass: 24450.818 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: AKU 1009a / Gene: cla-er / Production host: Escherichia coli (E. coli) / References: UniProt: U6C5W9
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Bis-Tris, 21%(w/v) PEG monomethyl ether 5000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 50917 / % possible obs: 96.8 % / Redundancy: 3.83 % / Biso Wilson estimate: 25.35 Å2 / Net I/σ(I): 17.52
Reflection shellResolution: 2→2.06 Å / Redundancy: 2.28 % / Mean I/σ(I) obs: 2.35 / % possible all: 84.2

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KQB

1kqb


Resolution: 2.005→19.895 Å / SU ML: 0.24 / σ(F): 1.98 / Phase error: 26.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 1989 3.91 %
Rwork0.1729 48912 -
obs0.175 50901 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.01 Å2 / Biso mean: 32.2559 Å2 / Biso min: 12.47 Å2
Refinement stepCycle: LAST / Resolution: 2.005→19.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 0 124 358 7106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086908
X-RAY DIFFRACTIONf_angle_d1.0419404
X-RAY DIFFRACTIONf_chiral_restr0.0411040
X-RAY DIFFRACTIONf_plane_restr0.0051204
X-RAY DIFFRACTIONf_dihedral_angle_d14.7292488
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0053-2.05540.3371300.28073152328288
2.0554-2.11090.28291410.23193462360397
2.1109-2.1730.26811360.21043544368097
2.173-2.2430.33171410.19753457359897
2.243-2.32310.25641500.19153487363797
2.3231-2.41590.26031440.18253510365497
2.4159-2.52570.26231430.18743518366198
2.5257-2.65850.25271390.18813497363698
2.6585-2.82470.25641490.18353507365698
2.8247-3.04210.27781390.1833568370798
3.0421-3.34690.2291500.17533536368699
3.3469-3.82820.20041380.15563563370199
3.8282-4.81180.15781460.13743542368899
4.8118-19.89630.18521430.15193569371299

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