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- PDB-3n2s: Structure of NfrA1 nitroreductase from B. subtilis -

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Basic information

Entry
Database: PDB / ID: 3n2s
TitleStructure of NfrA1 nitroreductase from B. subtilis
ComponentsNADPH-dependent nitro/flavin reductase
KeywordsOXIDOREDUCTASE / alpga-beta-alpha sandwich
Function / homology
Function and homology information


FMN reductase (NADPH) / FMN reductase (NADPH) activity
Similarity search - Function
Flavin oxidoreductase Frp family / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / FMN reductase (NADPH)
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMorera, S. / Gueguen-Chaignon, V. / Meyer, P. / Cortial, S. / Ouazzani, J.
CitationJournal: Febs Lett. / Year: 2010
Title: NADH oxidase activity of Bacillus subtilis nitroreductase NfrA1: insight into its biological role.
Authors: Cortial, S. / Chaignon, P. / Iorga, B.I. / Aymerich, S. / Truan, G. / Gueguen-Chaignon, V. / Meyer, P. / Morera, S. / Ouazzani, J.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent nitro/flavin reductase
B: NADPH-dependent nitro/flavin reductase
C: NADPH-dependent nitro/flavin reductase
D: NADPH-dependent nitro/flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,62910
Polymers114,7334
Non-polymers1,8966
Water7,062392
1
A: NADPH-dependent nitro/flavin reductase
B: NADPH-dependent nitro/flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3506
Polymers57,3662
Non-polymers9844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-98 kcal/mol
Surface area19230 Å2
MethodPISA
2
C: NADPH-dependent nitro/flavin reductase
D: NADPH-dependent nitro/flavin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2794
Polymers57,3662
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12140 Å2
ΔGint-79 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 54.810, 90.500
Angle α, β, γ (deg.)87.68, 87.64, 65.14
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
NADPH-dependent nitro/flavin reductase / NADPH-dependent oxidoreductase / NADPH-dependent FMN reductase / NADPH-dependent nitroreductase


Mass: 28683.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: Bacillus CNCM I-1915 / Gene: nfrA1, nfrA, ywcG, BSU38110, ipa-43d / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P39605, EC: 1.5.1.29
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 40.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 4000, 200mM sodium acetate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 64071 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 23.8
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 9.9 / Num. unique all: 8391 / Rsym value: 0.119 / % possible all: 86.6

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXSphasing
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→19.42 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.9248 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 3246 5.07 %RANDOM
Rwork0.1727 ---
obs0.174 64071 --
Displacement parametersBiso mean: 25.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.3541 Å2-0.0935 Å2-6.1003 Å2
2--3.5161 Å21.2554 Å2
3---0.8381 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7912 0 126 392 8430
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0182102
X-RAY DIFFRACTIONt_angle_deg1.03111292
X-RAY DIFFRACTIONt_dihedral_angle_d29492
X-RAY DIFFRACTIONt_trig_c_planes2832
X-RAY DIFFRACTIONt_gen_planes12395
X-RAY DIFFRACTIONt_it821020
X-RAY DIFFRACTIONt_nbd35
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion18.46
X-RAY DIFFRACTIONt_improper_torsion160
X-RAY DIFFRACTIONt_chiral_improper_torsion10655
X-RAY DIFFRACTIONt_ideal_dist_contact100394
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2134 201 4.74 %
Rwork0.176 4040 -
all0.1777 4241 -

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