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- PDB-2v15: Terbium binding in Streptococcus suis Dpr protein -

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Basic information

Entry
Database: PDB / ID: 2v15
TitleTerbium binding in Streptococcus suis Dpr protein
ComponentsDNA PROTECTION DURING STARVATION PROTEIN
KeywordsOXIDOREDUCTASE / IRON / DPS-FAMILY / FERROXIDASE / IRON-BINDING / PEROXIDE RESISTANCE / IRON STORAGE / METAL-BINDING / FERRITIN-LIKE
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
TERBIUM(III) ION / DNA protection during starvation protein / DNA protection during starvation protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHavukainen, H. / Papageorgiou, A.C. / Kauko, A.
CitationJournal: Protein Sci. / Year: 2008
Title: Structural basis of the zinc- and terbium-mediated inhibition of ferroxidase activity in Dps ferritin-like proteins.
Authors: Havukainen, H. / Haataja, S. / Kauko, A. / Pulliainen, A.T. / Salminen, A. / Haikarainen, T. / Finne, J. / Papageorgiou, A.C.
History
DepositionMay 22, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Mar 13, 2019Group: Data collection / Database references / Experimental preparation
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / struct_biol
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.5Dec 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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _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: DNA PROTECTION DURING STARVATION PROTEIN
B: DNA PROTECTION DURING STARVATION PROTEIN
C: DNA PROTECTION DURING STARVATION PROTEIN
D: DNA PROTECTION DURING STARVATION PROTEIN
E: DNA PROTECTION DURING STARVATION PROTEIN
F: DNA PROTECTION DURING STARVATION PROTEIN
G: DNA PROTECTION DURING STARVATION PROTEIN
H: DNA PROTECTION DURING STARVATION PROTEIN
I: DNA PROTECTION DURING STARVATION PROTEIN
J: DNA PROTECTION DURING STARVATION PROTEIN
K: DNA PROTECTION DURING STARVATION PROTEIN
L: DNA PROTECTION DURING STARVATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,06742
Polymers223,69212
Non-polymers3,37530
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42170 Å2
ΔGint-264.8 kcal/mol
Surface area76790 Å2
MethodPQS
Unit cell
Length a, b, c (Å)104.485, 137.715, 142.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
DNA PROTECTION DURING STARVATION PROTEIN / DPS-LIKE PEROXIDE RESISTANCE PROTEIN


Mass: 18641.014 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172
Source method: isolated from a genetically manipulated source
Details: N-TERMINUS TRUNCATED AND FIRST SEVEN RESIDUES REMOVED
Source: (gene. exp.) STREPTOCOCCUS SUIS (bacteria) / Strain: D282 / Plasmid: PET30EK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q4A3W3, UniProt: P0CB53*PLUS, Oxidoreductases; Oxidizing metal ions

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Non-polymers , 5 types, 649 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Tb
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.41 Å3/Da / Density % sol: 48.47 % / Description: NONE
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2UL AND 2UL VOLUME DROP, 30 % PEG 400, 0.2 M CACL2, 0.1 M HEPES-NAOH, PH 7.4, HANGING DROP,16C

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.06276
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2004 / Details: MIRRORS
RadiationMonochromator: TRIANGULAR HORIZONTAL- FOCUSING SI III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06276 Å / Relative weight: 1
ReflectionResolution: 2→28 Å / Num. obs: 115331 / % possible obs: 95.6 % / Observed criterion σ(I): 4.57 / Redundancy: 5.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9
Reflection shellHighest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKLdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMN

1umn


Resolution: 2.1→19.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.312 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 5761 5 %RANDOM
Rwork0.188 ---
obs0.19 109570 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.76 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14509 0 86 619 15214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214871
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.94920129
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9151822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.15825.082730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.754152534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2321559
X-RAY DIFFRACTIONr_chiral_restr0.0920.22203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.27934
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.210597
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2941
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.59319
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.468214534
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.51336342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.874.55595
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
Rfree0.315 381
Rwork0.244 7249

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