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- PDB-1veq: Mycobacterium smegmatis Dps Hexagonal form -

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Basic information

Entry
Database: PDB / ID: 1veq
TitleMycobacterium smegmatis Dps Hexagonal form
Componentsstarvation-induced DNA protecting protein
KeywordsDNA BINDING PROTEIN / DNA-binding protein
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: 3.98 Å
AuthorsRoy, S. / Gupta, S. / Das, S. / Sekar, K. / Chatterji, D. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: X-ray analysis of Mycobacterium smegmatis Dps and a comparative study involving other Dps and Dps-like molecules
Authors: Roy, S. / Gupta, S. / Das, S. / Sekar, K. / Chatterji, D. / Vijayan, M.
History
DepositionApr 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
K: starvation-induced DNA protecting protein
L: starvation-induced DNA protecting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,25624
Polymers243,58612
Non-polymers67012
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49060 Å2
ΔGint-337 kcal/mol
Surface area58590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.667, 194.667, 120.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
starvation-induced DNA protecting protein / Dps


Mass: 20298.809 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Plasmid: pET-Dps, pGEM-T Easy / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q8VP75, UniProt: P0C558*PLUS
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Calcium Chloride, 28% PEG 400, 0.1M Na-HEPES, pH 7.5, 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: Jul 1, 2003
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.98→20 Å / Num. all: 44121 / Num. obs: 20375 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.205 / Net I/σ(I): 4.6
Reflection shellResolution: 3.98→4.14 Å / Rmerge(I) obs: 0.478 / % possible all: 89.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cubic form of the Mycobacterium smegmatis Dps

Resolution: 3.98→19.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 8061584.77 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 911 4.5 %RANDOM
Rwork0.202 ---
obs0.202 20375 91.5 %-
all-20375 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso mean: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.04 Å2-24.42 Å20 Å2
2--4.04 Å20 Å2
3----8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.91 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 3.98→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14832 0 12 0 14844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.98→4.12 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 72 3.7 %
Rwork0.281 1855 -
obs-1855 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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