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- PDB-2wlu: Iron-bound crystal structure of Streptococcus pyogenes Dpr -

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Basic information

Entry
Database: PDB / ID: 2wlu
TitleIron-bound crystal structure of Streptococcus pyogenes Dpr
ComponentsDPS-LIKE PEROXIDE RESISTANCE PROTEIN
KeywordsOXIDOREDUCTASE / DNA-BINDING
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferroxidase / ferroxidase activity / 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
: / Non-specific DNA-binding protein / Peroxide resistance protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.94 Å
AuthorsHaikarainen, T. / Tsou, C.-C. / Wu, J.-J. / Papageorgiou, A.C.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2010
Title: Crystal Structures of Streptococcus Pyogenes Dpr Reveal a Dodecameric Iron-Binding Protein with a Ferroxidase Site.
Authors: Haikarainen, T. / Tsou, C.-C. / Wu, J.-J. / Papageorgiou, A.C.
#1: Journal: Infect.Immun. / Year: 2008
Title: An Iron-Binding Protein, Dpr, Decreases Hydrogen Peroxide Stress and Protects Streptococcus Pyogenes Against Multiple Stresses.
Authors: Tsou, C. / Chiang-Ni, C. / Lin, Y. / Chuang, W. / Lin, M. / Liu, C. / Wu, J.
History
DepositionJun 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 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 / 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 / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6926
Polymers19,3371
Non-polymers3555
Water4,017223
1
A: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)236,30272
Polymers232,04112
Non-polymers4,26160
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation82_656-y+1,z,-x+11
crystal symmetry operation31_665-z+1,-x+1,y1
crystal symmetry operation12_665-y+1,-z+3/2,x+1/21
crystal symmetry operation6_466z-1/2,-x+1,-y+3/21
crystal symmetry operation27_556-x+1/2,y,-z+3/21
crystal symmetry operation56_656-z+1,x+1/2,-y+3/21
crystal symmetry operation57_455y-1/2,z,x+1/21
crystal symmetry operation76_566x,-y+3/2,-z+3/21
crystal symmetry operation77_455z-1/2,x+1/2,y1
crystal symmetry operation35_466y-1/2,-z+3/2,-x+11
crystal symmetry operation50_565-x+1/2,-y+3/2,z1
Buried area42220 Å2
ΔGint-357.9 kcal/mol
Surface area68840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.268, 188.268, 188.268
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-1175-

NA

21A-2061-

HOH

31A-2117-

HOH

41A-2182-

HOH

51A-2183-

HOH

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Components

#1: Protein DPS-LIKE PEROXIDE RESISTANCE PROTEIN / NON-SPECIFIC DNA-BINDING PROTEIN


Mass: 19336.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q5XAZ8, UniProt: Q99YU7*PLUS, ferroxidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 7
Details: 0.1M HEPES PH 7.0, 1M SUCCINIC ACID PH 7.0, 1% W/V PEG 2000 MME, 5% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8132
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Feb 13, 2009 / Details: BENT, VERTICALLY FOCUSSING
RadiationMonochromator: SI (111), HORIZONTALLY FOCUSSING / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8132 Å / Relative weight: 1
ReflectionResolution: 1.93→43 Å / Num. obs: 20355 / % possible obs: 92.7 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / % possible all: 79.1

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Processing

Software
NameVersionClassification
REFMAC5.4.0078refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.94→43 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.754 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16394 1058 5.2 %RANDOM
Rwork0.14565 ---
obs0.14663 19295 93.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.381 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1283 0 20 223 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221374
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9711874
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3865184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36225.42459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.06415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.451154
X-RAY DIFFRACTIONr_chiral_restr0.0710.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021017
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_it0.4711.5852
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90721375
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5623522
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6564.5489
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: 1.942→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 96 -
Rwork0.206 1342 -
obs--90.96 %

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