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- PDB-4cy9: DpsA14 from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 4cy9
TitleDpsA14 from Streptomyces coelicolor
ComponentsDPSA
KeywordsIRON-BINDING PROTEIN / FERRITIN
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding
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
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.78 Å
AuthorsTownsend, P.D. / Hitchings, M.D. / Del Sol, R. / Pohl, E.
CitationJournal: Cell.Mol.Life Sci. / Year: 2014
Title: A Tale of Tails: Deciphering the Contribution of Terminal Tails to the Biochemical Properties of Two Dps Proteins from Streptomyces Coelicolor
Authors: Hitchings, M.D. / Townsend, P.D. / Pohl, E. / Facey, P.D. / Jones, D.H. / Dyson, P.J. / Del Sol, R.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2May 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 / struct_site
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 / _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: DPSA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4944
Polymers18,2181
Non-polymers2763
Water3,549197
1
A: DPSA
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)221,92848
Polymers218,61212
Non-polymers3,31536
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation82_555-y,z,-x1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation80_555-z,x,-y1
Buried area54280 Å2
ΔGint-260.8 kcal/mol
Surface area74490 Å2
MethodPQS
Unit cell
Length a, b, c (Å)209.660, 209.660, 209.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-2177-

HOH

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Components

#1: Protein DPSA / DPSA14


Mass: 18217.682 Da / Num. of mol.: 1 / Fragment: RESIDUES 4-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9R408
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDescription: NONE
Crystal growDetails: 0.2 M NACL, 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→48.1 Å / Num. obs: 38297 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 19.4

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.78→121.05 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.122 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.17088 1897 5 %RANDOM
Rwork0.15258 ---
obs0.15351 36339 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.379 Å2
Refinement stepCycle: LAST / Resolution: 1.78→121.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 18 197 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.0191374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.8251.9591880
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4665185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51323.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88815219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3151512
X-RAY DIFFRACTIONr_chiral_restr0.4230.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0211055
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 105 -
Rwork0.213 2407 -
obs--99.52 %

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