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- PDB-1umn: Crystal structure of Dps-like peroxide resistance protein (Dpr) f... -

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Basic information

Entry
Database: PDB / ID: 1umn
TitleCrystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis
ComponentsDPS-LIKE PEROXIDE RESISTANCE PROTEIN
KeywordsPEROXIDE RESISTANCE / IRON-BINDING / FERROXIDASE / DPS-FAMILY / 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
DNA protection during starvation protein / DNA protection during starvation protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKauko, A. / Haataja, S. / Pulliainen, A. / Finne, J. / Papageorgiou, A.C.
CitationJournal: J. Mol. Biol. / Year: 2004
Title: Crystal structure of Streptococcus suis Dps-like peroxide resistance protein Dpr: implications for iron incorporation.
Authors: Kauko, A. / Haataja, S. / Pulliainen, A.T. / Finne, J. / Papageorgiou, A.C.
History
DepositionAug 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
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
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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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
B: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
C: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
D: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
E: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
F: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
G: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
H: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
I: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
J: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
K: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
L: DPS-LIKE PEROXIDE RESISTANCE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,39335
Polymers223,69212
Non-polymers1,70123
Water30,3551685
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)104.735, 138.168, 142.707
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9953, -0.07049, -0.06643), (-0.06679, 0.00278, 0.99776), (-0.07015, 0.99751, -0.00747)19.46998, 136.02335, -135.58139
3given(-0.99911, -0.03159, 0.02778), (-0.02752, -0.00856, -0.99958), (0.03182, -0.99946, 0.00768)13.87208, 142.12906, 140.54878
4given(0.99401, 0.10028, 0.04342), (0.10048, -0.99494, -0.00247), (0.04295, 0.00682, -0.99905)-13.96115, 275.85297, 3.56415
5given(0.06817, -0.74062, -0.66846), (-0.7147, 0.43123, -0.55067), (0.6961, 0.51528, -0.49993)108.72004, 83.46333, -71.24289
6given(0.03164, -0.6731, -0.73887), (0.72065, -0.49688, 0.48351), (-0.69258, -0.54776, 0.46935)99.65805, 202.81387, 80.39436
7given(-0.07043, 0.66961, 0.73937), (0.68509, 0.57121, -0.45206), (-0.72504, 0.4747, -0.49897)-89.36369, 57.16426, -58.89568
8given(-0.03267, 0.74055, 0.67121), (-0.68937, -0.50295, 0.52135), (0.72367, -0.44568, 0.52695)-99.1459, 210.21654, 59.42184
9given(0.0751, -0.71551, 0.69455), (-0.74534, 0.42243, 0.51577), (-0.66244, -0.55641, -0.50158)101.94675, 82.22861, 83.60762
10given(-0.06875, 0.68925, -0.72126), (0.67386, 0.5652, 0.47588), (0.73565, -0.45331, -0.50331)-88.59692, 55.85215, 62.79881
11given(-0.02867, -0.68938, 0.72383), (0.74481, -0.49769, -0.44449), (0.66667, 0.52637, 0.52772)98.74805, 204.81123, -74.8491
12given(0.02491, 0.72113, -0.69235), (-0.67328, -0.49984, -0.54484), (-0.73896, 0.47972, 0.47308)-93.54265, 212.23178, -61.81357

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Components

#1: Protein
DPS-LIKE PEROXIDE RESISTANCE PROTEIN / DPR


Mass: 18641.014 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: N-TERMINUS TRUNCATED 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: Q9F5J9, UniProt: P0CB53*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1685 / 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: 2.3 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: HANGING DROP METHOD 2.0 UL 10 MG/ML PROTEIN + 2.0 UL RESERVOUR SOLUTION 27 % PEG 400, 0.2 M CACL2, 0.1M HEPES-NAOH, PH 7.4 +16C FEW DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 146502 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12
Reflection shellResolution: 1.95→2.01 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 1.7 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGH

1qgh


Resolution: 1.95→18.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3678334.77 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 7395 5.1 %RANDOM
Rwork0.185 ---
obs0.185 146414 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.3696 Å2 / ksol: 0.377455 e/Å3
Displacement parametersBiso mean: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å20 Å20 Å2
2---3.15 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.95→18.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14534 0 79 1685 16298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 1119 5.1 %
Rwork0.229 20902 -
obs--88.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3HEPES.PARHEPES.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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