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- PDB-3f7e: MSMEG_3380 F420 Reductase -

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Basic information

Entry
Database: PDB / ID: 3f7e
TitleMSMEG_3380 F420 Reductase
ComponentsPyridoxamine 5'-phosphate oxidase-related, FMN-binding
KeywordsUNKNOWN FUNCTION / F420 dependent reductase
Function / homology
Function and homology information


aflatoxin reductase (coenzyme F420) activity / coumarin catabolic process / aflatoxin catabolic process / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / cytosol
Similarity search - Function
F420-binding domain, putative / : / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
Pyridoxamine 5'-phosphate oxidase-related, FMN-binding
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.23 Å
AuthorsJackson, C.J.
CitationJournal: To be Published
Title: Identification and characterisation of two novel classes of F420-dependent reductases from Mycobacterium that degrade aflatoxin
Authors: Taylor, M.C. / Jackson, C.J. / Oakeshott, J.G.
History
DepositionNov 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding


Theoretical massNumber of molelcules
Total (without water)29,8232
Polymers29,8232
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-10.7 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.863, 65.347, 69.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-related, FMN-binding


Mass: 14911.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: MSMEG_3380 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0QXP8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10mM Tris, pH8.5, 20% PEG10000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 10, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.23→22 Å / Num. obs: 73957 / % possible obs: 97.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.69 Å2 / Rsym value: 0.072 / Net I/σ(I): 6.8
Reflection shellResolution: 1.23→1.3 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 10410 / Rsym value: 0.494 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.23→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.3 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19104 3725 5 %RANDOM
Rwork0.16693 ---
obs0.16816 70232 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.336 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.23→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2148 0 0 339 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9713044
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.135275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81623.173104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.01615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9981520
X-RAY DIFFRACTIONr_chiral_restr0.1120.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.21018
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21532
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2205
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8451.51390
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.42222229
X-RAY DIFFRACTIONr_scbond_it3.9073950
X-RAY DIFFRACTIONr_scangle_it4.6584.5815
X-RAY DIFFRACTIONr_rigid_bond_restr1.98622340
X-RAY DIFFRACTIONr_sphericity_free14.86510339
X-RAY DIFFRACTIONr_sphericity_bonded7.597102148
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 246 -
Rwork0.2 5017 -
obs--94.62 %

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