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- PDB-2yw7: Crystal structure of C-terminal deletion mutant of Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 2yw7
TitleCrystal structure of C-terminal deletion mutant of Mycobacterium smegmatis Dps
ComponentsStarvation-induced DNA protecting protein
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / Quarternary assebmly
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: 3.3 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: 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: Starvation-induced DNA protecting protein
B: Starvation-induced DNA protecting protein
C: Starvation-induced DNA protecting protein
D: Starvation-induced DNA protecting protein
E: Starvation-induced DNA protecting protein
F: Starvation-induced DNA protecting protein
G: Starvation-induced DNA protecting protein
H: Starvation-induced DNA protecting protein
I: Starvation-induced DNA protecting protein
J: Starvation-induced DNA protecting protein


Theoretical massNumber of molelcules
Total (without water)202,98810
Polymers202,98810
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21210 Å2
ΔGint-85 kcal/mol
Surface area60890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.516, 83.940, 111.911
Angle α, β, γ (deg.)90.00, 105.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Starvation-induced DNA protecting protein


Mass: 20298.809 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: pRSET-msdpsdeltaC26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0R692, UniProt: P0C558*PLUS

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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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG1140, 100mM CaCl2, 0.1M Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jan 20, 2006
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 24653 / % possible obs: 100 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.0108 / Net I/σ(I): 11.7
Reflection shellResolution: 3.3→3.382 Å / Rmerge(I) obs: 0.0331 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2467 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VEI

1vei


Resolution: 3.3→28.54 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.874 / SU B: 23.764 / SU ML: 0.399 / Cross valid method: THROUGHOUT / ESU R Free: 0.598 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25878 1320 5.1 %RANDOM
Rwork0.22179 ---
obs0.22367 24653 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.228 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.02 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 3.3→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11597 0 0 0 11597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02111837
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.95216082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.36351445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.35324.983578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.755152069
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2391560
X-RAY DIFFRACTIONr_chiral_restr0.0720.21842
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028922
X-RAY DIFFRACTIONr_nbd_refined0.260.26864
X-RAY DIFFRACTIONr_nbtor_refined0.3120.28041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2575
X-RAY DIFFRACTIONr_metal_ion_refined0.210.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.030.23
X-RAY DIFFRACTIONr_mcbond_it4.721.57409
X-RAY DIFFRACTIONr_mcangle_it6.052211678
X-RAY DIFFRACTIONr_scbond_it1.3634966
X-RAY DIFFRACTIONr_scangle_it2.344.54404
LS refinement shellResolution: 3.297→3.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 97 -
Rwork0.291 1690 -
obs--100 %

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