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- PDB-5j62: FMN-dependent Nitroreductase (CDR20291_0684) from Clostridium dif... -

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Basic information

Entry
Database: PDB / ID: 5j62
TitleFMN-dependent Nitroreductase (CDR20291_0684) from Clostridium difficile R20291
ComponentsPutative reductase
KeywordsOXIDOREDUCTASE / Nitroreductase / Hypervirulent / Clostridium difficile / R20291 / Metronidazole resistance
Function / homology
Function and homology information


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 / PHOSPHATE ION / Putative reductase
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWang, B. / Powell, S.M. / 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)53,2426
Polymers52,1432
Non-polymers1,1004
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7940 Å2
ΔGint-48 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.323, 100.323, 99.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative reductase


Mass: 26071.334 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_0684 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C9YJD4
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 0.1 M sodium citrate, pH 5.6 10% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 28386 / % possible obs: 100 % / Redundancy: 23.9 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.016 / Rrim(I) all: 0.078 / Χ2: 0.901 / Net I/av σ(I): 40.667 / Net I/σ(I): 6.6 / Num. measured all: 678045
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.1911.90.74213880.8160.2180.7750.8599.9
2.19-2.23160.69513930.8950.1760.7180.875100
2.23-2.27200.62913820.920.1420.6450.891100
2.27-2.3222.70.55714000.9530.1180.5690.875100
2.32-2.3724.50.50113770.9630.1020.5120.894100
2.37-2.4225.10.42213910.9770.0850.4310.89100
2.42-2.4825.20.36714170.9840.0740.3740.885100
2.48-2.5523.30.31313900.9850.0650.320.88699.9
2.55-2.6225.20.2713960.9910.0540.2750.89499.9
2.62-2.71270.23614030.9940.0460.240.91599.9
2.71-2.8126.80.18713970.9960.0360.190.91999.9
2.81-2.9226.50.15214120.9970.030.1550.9299.9
2.92-3.0526.30.12414150.9980.0240.1260.924100
3.05-3.2125.70.09814210.9990.020.10.924100
3.21-3.4123.60.07514260.9990.0160.0770.912100
3.41-3.6827.20.06142610.0120.0610.95100
3.68-4.0526.60.051143410.010.0520.933100
4.05-4.6325.50.043145610.0090.0440.893100
4.63-5.8324.50.04147610.0080.0410.824100
5.83-5023.70.032158610.0070.0320.91799.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-3000phasing
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ensemble model of 3PXV and 3EK3

3pxv

3ek3


Resolution: 2.15→35.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.389 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 1415 5 %RANDOM
Rwork0.1673 ---
obs0.1698 26891 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 129.2 Å2 / Biso mean: 45.286 Å2 / Biso min: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2--0.23 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 2.15→35.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 73 138 3470
Biso mean--35.89 44.56 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193401
X-RAY DIFFRACTIONr_bond_other_d0.0020.023235
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9564622
X-RAY DIFFRACTIONr_angle_other_deg1.0412.9837467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89625.364151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.60915589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6591516
X-RAY DIFFRACTIONr_chiral_restr0.1170.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213833
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02727
X-RAY DIFFRACTIONr_mcbond_it3.9984.2321671
X-RAY DIFFRACTIONr_mcbond_other3.9754.231670
X-RAY DIFFRACTIONr_mcangle_it5.4896.3212087
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 87 -
Rwork0.216 1951 -
all-2038 -
obs--99.76 %

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