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- PDB-2c2j: Crystal Structure Of The Dps92 From Deinococcus Radiodurans -

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Basic information

Entry
Database: PDB / ID: 2c2j
TitleCrystal Structure Of The Dps92 From Deinococcus Radiodurans
ComponentsDNA-BINDING STRESS RESPONSE PROTEIN
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / DPS / DEINOCOCCUS / RADIODURANS / DNA-BINDING
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function
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 2
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsCuypers, M.G. / Romao, C.V. / Mitchell, E. / McSweeney, S.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of the Dps2 from Deinococcus Radiodurans Reveals an Unusual Pore Profile with a Non-Specific Metal Binding Site.
Authors: Cuypers, M.G. / Mitchell, E.P. / Romao, C.V. / Mcsweeney, S.M.
History
DepositionSep 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,3703
Polymers23,2901
Non-polymers802
Water2,306128
1
A: DNA-BINDING STRESS RESPONSE PROTEIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)280,43836
Polymers279,47712
Non-polymers96224
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation7_665-z+1,-x+1,y1
crystal symmetry operation6_665z+1,-x+1,-y1
crystal symmetry operation10_656-y+1,z,-x+11
crystal symmetry operation12_654-y+1,-z,x-11
crystal symmetry operation11_656y+1,-z,-x+11
crystal symmetry operation9_654y+1,z,x-11
crystal symmetry operation8_645-z+1,x-1,-y1
crystal symmetry operation5_645z+1,x-1,y1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation2_755-x+2,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.453, 88.453, 88.453
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-1210-

FE

21A-2015-

HOH

31A-2044-

HOH

41A-2124-

HOH

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Components

#1: Protein DNA-BINDING STRESS RESPONSE PROTEIN / DRDPS92 / DPS FAMILY


Mass: 23289.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DRB0092 WAS TRUNCATED - RESIDUE NUMBERING STARTS AFTER N-TERMINAL RESIDUE NUMBER 30
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: Q9RZN1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.5 Å3/Da / Density % sol: 54.3 %
Crystal growpH: 7.5 / Details: 0.01M MGCL2, 0.05M TRIS-HCL PH 7.5, 5% ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC MARRESEARCH / Detector: CCD / Date: Mar 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.05→44.2 Å / Num. obs: 14773 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 21.1 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 40.4
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 18.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 5.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.05→88.74 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 2.587 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE 41 N-TERMINAL AND 5 C-TERMINAL RESIDUES ARE MISSING IN THE STRUCTURE. WATERS 22, 31, 43 AND 126 HAVE OCCUPANCIES BELOW 1 BECAUSE OF ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE 41 N-TERMINAL AND 5 C-TERMINAL RESIDUES ARE MISSING IN THE STRUCTURE. WATERS 22, 31, 43 AND 126 HAVE OCCUPANCIES BELOW 1 BECAUSE OF THEIR LOCALISATION ON SYMMETRY AXIS. Z22 LIES ON A CELL EDGE AND A 2 FOLD AXIS Z43 LIES ON A CELL EDGE AND A 2 FOLD AXIS Z126 LIES ON A 3 FOLD AXIS
RfactorNum. reflection% reflectionSelection details
Rwork0.179 ---
obs0.179 14753 100 %-
Rfree---RANDOM
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.91 Å2
Refinement stepCycle: LAST / Resolution: 2.05→88.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 2 128 1448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221345
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9361831
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.50925.63471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17715225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.898156
X-RAY DIFFRACTIONr_chiral_restr0.1030.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021040
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.2646
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2956
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3750.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1811.5846
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.81321330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7463570
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.164.5501
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: 2.05→2.1 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 -
Rwork0.202 1078

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