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- PDB-2ux1: Identification of two zinc-binding sites in the Streptococcus sui... -

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Basic information

Entry
Database: PDB / ID: 2ux1
TitleIdentification of two zinc-binding sites in the Streptococcus suis Dpr protein
ComponentsDNA PROTECTION DURING STARVATION PROTEIN
KeywordsOXIDOREDUCTASE / METAL-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 / DNA protection during starvation protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHavukainen, H. / Kauko, A. / Pulliainen, A.T. / Haataja, S. / Meyer-Klaucke, W. / Finne, J. / Papageorgiou, A.C.
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
DepositionMar 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 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 1.4Dec 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _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_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_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)225,59446
Polymers222,83912
Non-polymers2,75434
Water21,3121183
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39440 Å2
ΔGint-1123.5 kcal/mol
Surface area62830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.520, 137.690, 142.060
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: 18569.938 Da / Num. of mol.: 12 / Fragment: RESIDUES 8-172 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: N-TERMINUS TRUNCATED. FIRST SEVEN RESIDUES REMOVED. Q8G MUTATION
Source: (gene. exp.) STREPTOCOCCUS SUIS (bacteria) / Strain: D282 / Plasmid: PET30EK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9F5J9, UniProt: P0CB53*PLUS, Oxidoreductases; Oxidizing metal ions

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Non-polymers , 5 types, 1217 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1183 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 8 TO GLY ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN B, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN C, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN D, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN E, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN F, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN G, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN H, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN I, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN J, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN K, GLN 8 TO GLY ENGINEERED RESIDUE IN CHAIN L, GLN 8 TO GLY
Sequence detailsUNIPROT ENTRY HAS FULL LENGTH PROTEIN. PROTEIN DESCRIBED IN THIS PDB-ENTRY HAS TRUNCATED N-TERMINUS ...UNIPROT ENTRY HAS FULL LENGTH PROTEIN. PROTEIN DESCRIBED IN THIS PDB-ENTRY HAS TRUNCATED N-TERMINUS WITH FIRST 7 RESIDUES MISSING AND Q8G MUTATION.

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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: 2.31 Å3/Da / Density % sol: 46.28 % / Description: NONE
Crystal growpH: 7.3
Details: PROTEIN WAS CRYSTALLIZED FROM 30% PEG 400, 0.2 M CACL2, 0.1 M HEPES-NA, PH 7.4 AND 1 MM ZNCL2.

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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: Apr 2, 2005 / 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: 1.8→19.97 Å / Num. obs: 180247 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.004 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.98
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.78 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / % possible all: 99.4

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Processing

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

1umn


Resolution: 1.8→19.97 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.651 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 8779 4.6 %RANDOM
Rwork0.206 ---
obs0.208 180247 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: 31.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20 Å2
2---1.2 Å20 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14496 0 90 1183 15769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02214918
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.94920207
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.54751839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.01925.027730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.333152543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9331561
X-RAY DIFFRACTIONr_chiral_restr0.0760.22213
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211344
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.28213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.210610
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.21231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.59363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.093214602
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.94936331
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9674.55600
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.351 655
Rwork0.298 12957

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