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- PDB-2c6r: FE-SOAKED CRYSTAL STRUCTURE OF THE DPS92 FROM DEINOCOCCUS RADIODURANS -

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Basic information

Entry
Database: PDB / ID: 2c6r
TitleFE-SOAKED CRYSTAL STRUCTURE OF THE DPS92 FROM DEINOCOCCUS RADIODURANS
ComponentsDNA-BINDING STRESS RESPONSE PROTEIN, DPS FAMILY
KeywordsDNA BINDING PROTEIN / DPS / DEINOCOCCUS / RADIODURANS / DNA-BINDING PROTEIN
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: 2.1 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
DepositionNov 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 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_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
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, DPS FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6047
Polymers23,2901
Non-polymers3156
Water2,432135
1
A: DNA-BINDING STRESS RESPONSE PROTEIN, DPS FAMILY
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)283,25384
Polymers279,47712
Non-polymers3,77672
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)88.965, 88.965, 88.965
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-2014-

HOH

21A-2031-

HOH

31A-2132-

HOH

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Components

#1: Protein DNA-BINDING STRESS RESPONSE PROTEIN, DPS FAMILY / 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 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.: 5 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2.52 Å3/Da / Density % sol: 54.3 %
Crystal growpH: 7.5
Details: 0.01M MGCL2, 0.05M TRIS PH7.5, 5% ISOPROPANOL, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.1070,1.7399
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.1071
21.73991
ReflectionResolution: 2.1→29.66 Å / Num. obs: 13986 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→89.09 Å / Cor.coef. Fo:Fc: 0.957 / SU B: 3.411 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rwork0.188 --
obs0.188 13986 99.9 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1318 0 6 135 1459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221363
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9371859
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5375170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14125.69472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8915232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.035156
X-RAY DIFFRACTIONr_chiral_restr0.1110.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021056
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2654
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2942
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2102
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.273
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0731.5859
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72121348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5033577
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.894.5508
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0 0
Rwork0.244 1023

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