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- PDB-3h96: Msmeg_3358 F420 Reductase -

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Basic information

Entry
Database: PDB / ID: 3h96
TitleMsmeg_3358 F420 Reductase
ComponentsF420-H2 Dependent Reductase A
KeywordsFLAVOPROTEIN / PNPOX / F420 / Flavin / Reductase / Aflatoxin
Function / homologyF420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / oxidoreductase activity / Roll / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJackson, C.J. / French, N. / Newman, J. / Taylor, M.C. / Russell, R.J. / Oakeshott, J.G.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Identification and characterization of two families of F420 H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation.
Authors: Taylor, M.C. / Jackson, C.J. / Tattersall, D.B. / French, N. / Peat, T.S. / Newman, J. / Briggs, L.J. / Lapalikar, G.V. / Campbell, P.M. / Scott, C. / Russell, R.J. / Oakeshott, J.G.
History
DepositionApr 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F420-H2 Dependent Reductase A
B: F420-H2 Dependent Reductase A
C: F420-H2 Dependent Reductase A
D: F420-H2 Dependent Reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6255
Polymers62,5634
Non-polymers621
Water6,269348
1
A: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: F420-H2 Dependent Reductase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7032
Polymers15,6411
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: F420-H2 Dependent Reductase A


Theoretical massNumber of molelcules
Total (without water)15,6411
Polymers15,6411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.650, 71.150, 63.840
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
F420-H2 Dependent Reductase A


Mass: 15640.764 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: MC2 / Gene: MSMEG_3356 / Plasmid: pDEST 17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: A0QXM5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 36 w/v polyethylene glycol monomethyl ether 5000, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979461 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: double crystal monochromator with sagitally bent second crystal horizontal focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979461 Å / Relative weight: 1
ReflectionResolution: 2→47.51 Å / Num. obs: 34129 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.174 / Mean I/σ(I) obs: 7.2 / % possible all: 91.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→45.7 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.909 / SU B: 9.917 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25508 2674 8 %RANDOM
Rwork0.18451 ---
obs0.18939 30897 92.6 %-
all-30897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.835 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å2-1.57 Å2
2---0.46 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 4 348 4554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0224403
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8481.9386021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.48223.116199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.58115658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9091536
X-RAY DIFFRACTIONr_chiral_restr0.1310.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213454
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4691.52774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37324479
X-RAY DIFFRACTIONr_scbond_it3.08631629
X-RAY DIFFRACTIONr_scangle_it4.7834.51532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 654 -
Rwork0.189 1146 -
obs--67.57 %
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)
10.31550.09920.24910.28340.00120.2205-0.0027-0.0212-0.0003-0.033-0.003-0.01510.0043-0.01590.00570.0271-0.00270.00680.0280.00350.01251.9535.5531.277
20.49620.1765-0.09280.33920.11180.09350.01250.0292-0.00990.0193-0.0091-0.00780.0046-0.0106-0.00350.02350.00440.00620.0396-0.00270.0056-7.7047.029-30.672
30.2481-0.11950.04370.50990.05660.0220.0020.01540.02340.0129-0.0103-0.01290.0067-0.00070.00830.0261-0.00410.01120.02690.00080.015522.1165.688-41.1
40.6573-0.2146-0.19770.3986-0.03060.08840.0286-0.0207-0.0007-0.0274-0.0260.0016-0.00440.0065-0.00260.0160.00030.00750.0518-0.00280.004431.856.928-9.407
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 142
2X-RAY DIFFRACTION2B6 - 142
3X-RAY DIFFRACTION3C6 - 142
4X-RAY DIFFRACTION4D6 - 142

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