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- PDB-5h46: Mycobacterium smegmatis Dps1 mutant - F47E -

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Basic information

Entry
Database: PDB / ID: 5h46
TitleMycobacterium smegmatis Dps1 mutant - F47E
ComponentsDNA protection during starvation protein
KeywordsOXIDOREDUCTASE / Structural switch / Mutational tipping point / Point mutant / Oligomerisation
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsWilliams, S.M. / Chandran, A.V. / Vijayan, M. / Chatterji, D.
Funding support India, 1items
OrganizationGrant numberCountry
India
Citation
Journal: Structure / Year: 2017
Title: A Mutation Directs the Structural Switch of DNA Binding Proteins under Starvation to a Ferritin-like Protein Cage.
Authors: Williams, S.M. / Chandran, A.V. / Prakash, S. / Vijayan, M. / Chatterji, D.
#1: Journal: Biochemistry / Year: 2008
Title: Molecular mechanism of in vitro oligomerization of Dps from Mycobacterium smegmatis: mutations of the residues identified by "interface cluster" analysis.
Authors: Chowdhury, R.P. / Vijayabaskar, M.S. / Vishveshwara, S. / Chatterji, D.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 8, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA protection during starvation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9834
Polymers16,8161
Non-polymers1683
Water18010
1
A: DNA protection during starvation protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)407,60396
Polymers403,58224
Non-polymers4,02172
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area56770 Å2
ΔGint-374 kcal/mol
Surface area137390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.070, 175.070, 175.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-201-

FE2

21A-202-

FE2

31A-203-

FE2

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Components

#1: Protein DNA protection during starvation protein


Mass: 16815.914 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 9-157 / Mutation: F47E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: dps, MSMEG_6467, MSMEI_6295 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: A0R692, Oxidoreductases; Oxidizing metal ions
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7.5 / Details: 100 mM Na-HEPES, 200 mM CaCl2, 10% PEG 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.85→39.147 Å / Num. obs: 5200 / % possible obs: 99.9 % / Redundancy: 42.7 % / Net I/σ(I): 30.3
Reflection shellResolution: 3→3.16 Å / CC1/2: 0.68

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
REFMACdata reduction
REFMACdata scaling
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VEI

1vei


Resolution: 2.85→39.147 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 38.363 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R: 1.085 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26025 583 10.1 %RANDOM
Rwork0.22863 ---
obs0.23194 5200 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.235 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.85→39.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 3 10 1185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191193
X-RAY DIFFRACTIONr_bond_other_d0.0050.021107
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9571623
X-RAY DIFFRACTIONr_angle_other_deg1.07432564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6045148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.83225.34558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2615205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.192156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021330
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02224
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_it5.9718.037595
X-RAY DIFFRACTIONr_mcbond_other5.9258.036594
X-RAY DIFFRACTIONr_mcangle_it9.30112.031742
X-RAY DIFFRACTIONr_mcangle_other9.30812.036743
X-RAY DIFFRACTIONr_scbond_it5.9328.496598
X-RAY DIFFRACTIONr_scbond_other5.938.481596
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.58712.566881
X-RAY DIFFRACTIONr_long_range_B_refined16.3895120
X-RAY DIFFRACTIONr_long_range_B_other16.3915118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.851→2.925 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 40 -
Rwork0.353 378 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 10.6125 Å / Origin y: -36.9431 Å / Origin z: -29.8096 Å
111213212223313233
T0.327 Å20.0535 Å20.0173 Å2-0.1152 Å2-0.1397 Å2--0.2011 Å2
L2.4959 °20.6065 °2-0.3533 °2-0.4498 °2-0.2995 °2--0.202 °2
S-0.1457 Å °0.1475 Å °-0.3729 Å °-0.1733 Å °0.0459 Å °-0.1362 Å °0.1015 Å °-0.0254 Å °0.0998 Å °

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