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- PDB-2wzw: Crystal structure of the FMN-dependent nitroreductase NfnB from M... -

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Basic information

Entry
Database: PDB / ID: 2wzw
TitleCrystal structure of the FMN-dependent nitroreductase NfnB from Mycobacterium smegmatis in complex with NADPH
ComponentsNFNB PROTEIN
KeywordsOXIDOREDUCTASE / NITROREDUCTASE
Function / homology
Function and homology information


Oxidoreductases / xenobiotic catabolic process / FMN binding / NADP binding / oxidoreductase activity / protein homodimerization activity / identical protein 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 / Chem-NDP / PHOSPHATE ION / Nitroreductase NfnB
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBellinzoni, M. / Manina, G. / Riccardi, G. / Alzari, P.M.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Biological and Structural Characterization of the Mycobacterium Smegmatis Nitroreductase Nfnb, and its Role in Benzothiazinone Resistance
Authors: Manina, G. / Bellinzoni, M. / Pasca, M.R. / Neres, J. / Milano, A. / Ribeiro, A.L. / Buroni, S. / Skovierova, H. / Dianiskova, P. / Mikusova, K. / Marak, J. / Makarov, V. / Giganti, D. / ...Authors: Manina, G. / Bellinzoni, M. / Pasca, M.R. / Neres, J. / Milano, A. / Ribeiro, A.L. / Buroni, S. / Skovierova, H. / Dianiskova, P. / Mikusova, K. / Marak, J. / Makarov, V. / Giganti, D. / Haouz, A. / Lucarelli, A.P. / Degiacomi, G. / Piazza, A. / Chiarelli, L.R. / De Rossi, E. / Salina, E. / Cole, S.T. / Alzari, P.M. / Riccardi, G.
History
DepositionDec 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NFNB PROTEIN
B: NFNB PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8218
Polymers51,8782
Non-polymers1,9436
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11260 Å2
ΔGint-77.2 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.550, 115.610, 119.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1236-

PO4

21A-2160-

HOH

31B-2181-

HOH

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Components

#1: Protein NFNB PROTEIN / NITROREDUCTASE NFNB


Mass: 25939.205 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / Plasmid: PET-28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0R6D0
#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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST GLY RESIDUE IS A PURIFICATION TAG LEFTOVER

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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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 8
Details: 20% (W/V) PEG8000, 6% (V/V) ISOPROPANOL, 200 MM NH4H2PO4, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 19, 2009 / Details: PT COATED MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.8→59.8 Å / Num. obs: 55133 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.46 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.9.3refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WZV

2wzv


Resolution: 1.8→45.12 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9445 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.089 / SU Rfree Blow DPI: 0.085 / SU Rfree Cruickshank DPI: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN ISOTROPIC EQUIVALENTS OF THE SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 2795 5.07 %RANDOM
Rwork0.1497 ---
obs0.1508 55131 99.92 %-
Displacement parametersBiso mean: 23.07 Å2
Baniso -1Baniso -2Baniso -3
1-4.1919 Å20 Å20 Å2
2---1.0964 Å20 Å2
3----3.0954 Å2
Refine analyzeLuzzati coordinate error obs: 0.164 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 125 373 3930
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.95110HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1320SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it3670HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion15.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion477SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4532SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2057 205 5.08 %
Rwork0.1901 3830 -
all0.1909 4035 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1453-0.1957-0.06990.6417-0.00680.502-0.00440.16860.2484-0.0571-0.02810.0441-0.0699-0.05040.03250.04490.0043-0.00440.06740.02760.0738-28.029-84.736-29.222
23.4578-0.36860.31380.9568-0.11562.3598-0.1195-0.01360.58130.1067-0.0957-0.0353-0.20240.10430.21520.0708-0.0243-0.02960.0417-0.02380.3029-10.125-75.302-19.379
321.828315.26981.061114.28090.501900.1363-1.51611.67070.5351-0.38740.3362-0.2793-0.18460.25110.15710.0116-0.05730.173-0.09970.5238-17.77-63.793-26.295
41.3193-0.25880.40280.5782-0.21080.42-0.02270.07490.2024-0.012-0.014-0.0127-0.02450.00280.03680.0253-0.00280.00860.02170.01040.0652-22.858-84.621-24.53
50.5685-0.37360.01980.99150.14420.5085-0.03420.0195-0.03350.06080.0235-0.07260.1170.05280.01070.04930.00750.01640.0426-0.00530.0431-11.865-103.588-18.701
600.40880.59548.7539-7.234232.97350.0931-0.0174-0.05510.3576-0.1707-0.52570.0364-3.78670.07760.21060.02870.02470.4435-0.02410.2798-32.697-95.092-5.368
72.0953-0.46840.19014.3734-1.83252.3245-0.091-0.231-0.16110.39960.12770.41710.072-0.1489-0.03670.1368-0.04290.07490.14880.01690.1003-32.508-112.397-12.034
80.7275-0.3285-0.05030.9167-0.08230.3338-0.01740.00250.02160.04140.01470.01750.05110.00780.00270.0401-0.00350.00960.0249-0.01480.0164-18.143-101.954-16.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 13:91)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 92:119)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 120:132)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 133:234)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 12:91)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 92:98)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 99:127)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 128:234)

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