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- PDB-2yw6: Structural studies of N terminal deletion mutant of Dps from Myco... -

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Basic information

Entry
Database: PDB / ID: 2yw6
TitleStructural studies of N terminal deletion mutant of Dps from Mycobacterium smegmatis
ComponentsDNA protection during starvation protein
KeywordsOXIDOREDUCTASE / DNA-BINDING PROTEIN / Quarternary assembly / Ferroxidation
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 / DNA protection during starvation protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsRoy, S. / Saraswathi, R. / Gupta, S. / Sekar, K. / Chatterji, D. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Role of N and C-terminal Tails in DNA Binding and Assembly in Dps: Structural Studies of Mycobacterium smegmatis Dps Deletion Mutants
Authors: Roy, S. / Saraswathi, R. / Gupta, S. / Sekar, K. / Chatterji, D. / Vijayan, M.
History
DepositionApr 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)60,8963
Polymers60,8963
Non-polymers00
Water3,333185
1
A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein

A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein

A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein

A: DNA protection during starvation protein
B: DNA protection during starvation protein
C: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)243,58612
Polymers243,58612
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
crystal symmetry operation12_565x,x-y+1,-z+1/31
Buried area36040 Å2
ΔGint-147 kcal/mol
Surface area62150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.443, 87.443, 212.537
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein DNA protection during starvation protein / DNA binding protein from stationary phase cells


Mass: 20298.809 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: dps / Plasmid: pET-msdpsdelta9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q8VP75, UniProt: P0C558*PLUS, Oxidoreductases; Oxidizing metal ions
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 293 K / Method: microbath under oil / pH: 8
Details: protein buffer in 50mM Tris-HCl (pH8.0), 0.2M Calcium chloride, 0.1M HEPES-Na pH7.5, 28% polyethelene glycol 400, Microbath under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2005
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→30 Å / Num. obs: 15936 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Redundancy: 17 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 28
Reflection shellResolution: 2.53→2.69 Å / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 3.83 / Num. unique all: 1411 / % possible all: 88.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VEI

1vei


Resolution: 2.53→28.62 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2414985.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 776 4.9 %RANDOM
Rwork0.229 ---
obs0.229 15897 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.6917 Å2 / ksol: 0.374647 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20.58 Å20 Å2
2--3.78 Å20 Å2
3----2.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.53→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 0 185 3740
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it3.311.5
X-RAY DIFFRACTIONc_mcangle_it5.462
X-RAY DIFFRACTIONc_scbond_it4.122
X-RAY DIFFRACTIONc_scangle_it6.782.5
LS refinement shellResolution: 2.53→2.69 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 130 5.4 %
Rwork0.311 2260 -
obs-2260 88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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