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- PDB-5j6c: FMN-dependent Nitroreductase (CDR20291_0767) from Clostridium dif... -

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Basic information

Entry
Database: PDB / ID: 5j6c
TitleFMN-dependent Nitroreductase (CDR20291_0767) from Clostridium difficile R20291
ComponentsPutative reductase
KeywordsOXIDOREDUCTASE / Nitroreductase / Hypervirulent / Metronidazole resistance
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / IMIDAZOLE / Putative reductase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsPowell, S.M. / Wang, B. / Hessami, N. / Najar, F.Z. / Thomas, L.M. / West, A.H. / Karr, E.A. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
Price Family Foundation United States
CitationJournal: Nitric Oxide / Year: 2016
Title: Crystal structures of two nitroreductases from hypervirulent Clostridium difficile and functionally related interactions with the antibiotic metronidazole.
Authors: Wang, B. / Powell, S.M. / Hessami, N. / Najar, F.Z. / Thomas, L.M. / Karr, E.A. / West, A.H. / Richter-Addo, G.B.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 2023Group: 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: Putative reductase
B: Putative reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6526
Polymers46,6022
Non-polymers1,0514
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-24 kcal/mol
Surface area13770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.908, 70.732, 87.882
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative reductase


Mass: 23300.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain R20291) (bacteria)
Strain: R20291 / Gene: CDR20291_0767 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: C9YJL7
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M di-hydrogen ammonium citrate 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jul 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 25340 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 22.72 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.067 / Rrim(I) all: 0.129 / Χ2: 1.264 / Net I/av σ(I): 12.64 / Net I/σ(I): 5.8 / Num. measured all: 86479
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.10.45412600.8140.2950.5440.93299.4
2.14-2.183.20.4212150.8460.2710.5020.94198.7
2.18-2.223.20.38312490.8540.2480.4580.93299.4
2.22-2.263.30.33212490.8870.2110.3950.93199.6
2.26-2.313.40.33612530.8920.2110.3990.91899.5
2.31-2.373.40.29312460.9320.1820.3460.95299.4
2.37-2.423.50.28612410.9310.1770.3380.96799.7
2.42-2.493.50.23912520.9540.1440.2810.95199.4
2.49-2.563.50.21312600.960.1280.250.96699.5
2.56-2.653.50.21412660.9630.130.2521.01599.6
2.65-2.743.50.17612530.9720.1070.2071.00299.5
2.74-2.853.60.15712650.980.0940.1841.05699.3
2.85-2.983.50.14412590.980.0880.171.09799.8
2.98-3.143.50.12912710.9840.0780.1511.15999.5
3.14-3.333.60.09512600.9880.0570.1111.25599.4
3.33-3.593.50.07612840.990.0460.0891.58999.9
3.59-3.953.50.06812840.9910.0410.081.82598.8
3.95-4.523.40.06712850.990.0420.082.15399.3
4.52-5.73.30.06713040.9910.0420.0792.15298.9
5.7-5030.06413840.990.0430.0782.45298

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M5K

3m5k


Resolution: 2.096→43.941 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2409 1768 7.91 %
Rwork0.1856 20584 -
obs0.1899 22352 87.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.08 Å2 / Biso mean: 25.0279 Å2 / Biso min: 12.71 Å2
Refinement stepCycle: final / Resolution: 2.096→43.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 72 124 3010
Biso mean--21.75 26.74 -
Num. residues----346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072938
X-RAY DIFFRACTIONf_angle_d0.9143950
X-RAY DIFFRACTIONf_chiral_restr0.057424
X-RAY DIFFRACTIONf_plane_restr0.004488
X-RAY DIFFRACTIONf_dihedral_angle_d18.2691774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0964-2.1530.2851280.231452158082
2.153-2.21640.28381220.20991481160383
2.2164-2.28790.25931360.20631513164986
2.2879-2.36970.27291220.20471496161884
2.3697-2.46460.33911250.21041458158382
2.4646-2.57670.29631260.21081472159882
2.5767-2.71250.30181380.20941491162984
2.7125-2.88250.29911280.21311478160683
2.8825-3.1050.26831270.21631548167585
3.105-3.41730.25121480.19521724187295
3.4173-3.91160.21081550.15931797195299
3.9116-4.92710.16851570.14241784194197
4.9271-43.95060.20891560.17691890204697

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