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- PDB-2f7n: Structure of D. radiodurans Dps-1 -

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Basic information

Entry
Database: PDB / ID: 2f7n
TitleStructure of D. radiodurans Dps-1
ComponentsDNA-binding stress response protein, Dps family
KeywordsDNA BINDING PROTEIN / 4-helix bundle
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 1
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsLee, Y.H. / Kim, S.G. / Bhattacharyya, G. / Grove, A.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of Dps-1, a functionally distinct Dps protein from Deinococcus radiodurans.
Authors: Kim, S.G. / Bhattacharyya, G. / Grove, A. / Lee, Y.H.
History
DepositionDec 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Feb 14, 2024Group: 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding stress response protein, Dps family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3836
Polymers23,0511
Non-polymers3325
Water2,072115
1
A: DNA-binding stress response protein, Dps family
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)140,29536
Polymers138,3046
Non-polymers1,99130
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation11_465y-1,-z+1,-x1
2
A: DNA-binding stress response protein, Dps family
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)280,59072
Polymers276,60912
Non-polymers3,98260
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation5_564z,x+1,y-11
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation7_564-z,-x+1,y-11
crystal symmetry operation8_566-z,x+1,-y+11
crystal symmetry operation9_465y-1,z+1,x1
crystal symmetry operation10_665-y+1,z+1,-x1
crystal symmetry operation11_465y-1,-z+1,-x1
crystal symmetry operation12_665-y+1,-z+1,x1
Buried area60380 Å2
ΔGint-734 kcal/mol
Surface area59130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.130, 90.130, 90.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-208-

CO

21A-211-

CO

31A-301-

SO4

41A-301-

SO4

51A-286-

HOH

61A-322-

HOH

71A-331-

HOH

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Components

#1: Protein DNA-binding stress response protein, Dps family / Dps-1 Iron sequester ferritin homolog


Mass: 23050.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 15807254, UniProt: Q9RS64*PLUS
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM MES; 100mM cobalt chloride; 2M anmmonium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 2005
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 31997 / Num. obs: 16568 / % possible obs: 99.8 % / Observed criterion σ(I): 5 / Redundancy: 9.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 90.3

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3025 10 %Random
Rwork0.195 ---
all0.2 16568 --
obs0.2 16568 --
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 9 115 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_mcbond_it0.8791.5
X-RAY DIFFRACTIONc_mcangle_it1.3312
X-RAY DIFFRACTIONc_scbond_it1.5622
X-RAY DIFFRACTIONc_scangle_it2.1642.5

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