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- PDB-2c2u: Dps from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 2c2u
TitleDps from Deinococcus radiodurans
ComponentsDNA-BINDING STRESS RESPONSE PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DPS / IRON / DEINOCOCCUS RADIODURANS / DNA-BINDING
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsRomao, C.V. / Mitchell, E. / McSweeney, S.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2006
Title: The Crystal Structure of Deinococcus Radiodurans Dps Protein (Dr2263) Reveals the Presence of a Novel Metal Centre in the N Terminus.
Authors: Romao, C.V. / Mitchell, E. / Mcsweeney, S.
History
DepositionSep 30, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-BINDING STRESS RESPONSE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2684
Polymers23,0511
Non-polymers2173
Water6,197344
1
A: DNA-BINDING STRESS RESPONSE PROTEIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)279,21648
Polymers276,60912
Non-polymers2,60836
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation6_566z,-x+1,-y+11
crystal symmetry operation12_665-y+1,-z+1,x1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation11_566y,-z+1,-x+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation8_656-z+1,x,-y+11
crystal symmetry operation3_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)90.369, 90.369, 90.369
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-1208-

SO4

21A-1208-

SO4

31A-1210-

FE

41A-2065-

HOH

51A-2090-

HOH

61A-2096-

HOH

71A-2151-

HOH

81A-2165-

HOH

91A-2314-

HOH

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Components

#1: Protein DNA-BINDING STRESS RESPONSE PROTEIN / DPS


Mass: 23050.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RS64
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 8.5
Details: 200MM LITHIUM SULFATE 100MM TRIS-HCL PH8.5 15% PEG4000, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 24, 2005 / Details: MULTI-LAYER MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.1→21.31 Å / Num. obs: 99021 / % possible obs: 99.6 % / Observed criterion σ(I): 2.5 / Redundancy: 5.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.1→1.13 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C2F

2c2f


Resolution: 1.1→21.3 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.663 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 29 AMINO ACID RESIDUES WERE NOT MODELLED DUE TO THE FACT THAT WAS NOT POSSIBLE TO ALLOCATE THE ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.149 4931 5 %RANDOM
Rwork0.126 ---
obs0.127 94077 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.05 Å2
Refinement stepCycle: LAST / Resolution: 1.1→21.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 7 344 1767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211538
X-RAY DIFFRACTIONr_bond_other_d0.0020.021381
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.952093
X-RAY DIFFRACTIONr_angle_other_deg1.98333210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8215177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.71524.19493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3021516
X-RAY DIFFRACTIONr_chiral_restr0.1240.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021714
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02320
X-RAY DIFFRACTIONr_nbd_refined0.2680.2370
X-RAY DIFFRACTIONr_nbd_other0.2280.21348
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2770
X-RAY DIFFRACTIONr_nbtor_other0.0770.2857
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3560.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0351.51168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.24321475
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3583724
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.454.5618
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.13 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.215 331
Rwork0.209 6807

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