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- PDB-4qlx: Crystal structure of CLA-ER with product binding -

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Basic information

Entry
Database: PDB / ID: 4qlx
TitleCrystal structure of CLA-ER with product binding
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / NADH oxidase/flavin reductase family / enone reductase / KetoC / FMN
Function / homology
Function and homology information


NADH dehydrogenase / 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 / 10-oxooctadecanoic acid / Nitroreductase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Nitroreductase family protein
B: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,58911
Polymers48,9022
Non-polymers1,6879
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-77 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.933, 68.850, 197.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

21B-533-

HOH

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Components

#1: Protein Nitroreductase family protein / CLA-ER


Mass: 24450.818 Da / Num. of mol.: 2
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, Oxidoreductases
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-KTC / 10-oxooctadecanoic acid


Mass: 298.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 100mM sodium cacodylate, 200mM NaCl, 2.0M ammonium sulfate, pH 6.8, 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
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 32720 / % possible obs: 99.7 % / Redundancy: 7.08 % / Biso Wilson estimate: 23.33 Å2 / Net I/σ(I): 11.93
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.3 % / Mean I/σ(I) obs: 2.49 / % possible all: 80.6

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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: 4QLY

4qly


Resolution: 1.95→19.902 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2012 6.15 %
Rwork0.1868 30695 -
obs0.1895 32707 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.35 Å2 / Biso mean: 27.2378 Å2 / Biso min: 9.82 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.902 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3363 0 109 280 3752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083545
X-RAY DIFFRACTIONf_angle_d1.0634812
X-RAY DIFFRACTIONf_chiral_restr0.043528
X-RAY DIFFRACTIONf_plane_restr0.005615
X-RAY DIFFRACTIONf_dihedral_angle_d14.5611296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.99870.30921520.248921402292
1.9987-2.05270.27711380.233221982336
2.0527-2.1130.27241350.213721432278
2.113-2.18120.24851450.197821562301
2.1812-2.2590.26061440.201821992343
2.259-2.34930.24981410.200321692310
2.3493-2.45610.2861420.201221622304
2.4561-2.58530.20561400.19121742314
2.5853-2.74690.2471530.201421812334
2.7469-2.95840.27091390.198622142353
2.9584-3.25490.2941390.201621822321
3.2549-3.72320.1841450.171522112356
3.7232-4.68080.18281460.148622472393
4.6808-19.90260.19411530.173223192472

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