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- PDB-2bw1: Iron-bound crystal structure of Dps-like peroxide resistance prot... -

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Basic information

Entry
Database: PDB / ID: 2bw1
TitleIron-bound crystal structure of Dps-like peroxide resistance protein (Dpr) from Streptococcus suis.
ComponentsDPS-LIKE PEROXIDE RESISTANCE PROTEIN
KeywordsPEROXIDE RESISTANCE / DPR / 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: 1.81 Å
AuthorsKauko, A. / Pulliainen, A. / Haataja, S. / Finne, J. / Papageorgiou, A.C.
CitationJournal: J. Mol. Biol. / Year: 2006
Title: Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core.
Authors: Kauko, A. / Pulliainen, A.T. / Haataja, S. / Meyer-Klaucke, W. / Finne, J. / Papageorgiou, A.C.
History
DepositionJul 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2006Provider: 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: Advisory / Data collection ...Advisory / Data collection / Database references / Experimental preparation / Other
Category: citation / citation_author ...citation / citation_author / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_validate_polymer_linkage / 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 / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5May 1, 2024Group: 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: 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)224,50329
Polymers222,83912
Non-polymers1,66317
Water27,0591502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.130, 138.050, 142.550
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(-0.99219, -0.09213, -0.0841), (-0.08445, -8.0E-5, 0.99643), (-0.0918, 0.99575, -0.0077)22.40622, 136.30128, -135.0296
2given(-0.99871, -0.0378, 0.03383), (-0.03354, -0.00818, -0.9994), (0.03805, -0.99925, 0.0069)14.65724, 142.10468, 140.49066
3given(0.99064, 0.12423, 0.05648), (0.12443, -0.99223, -5.0E-5), (0.05604, 0.00708, -0.9984)-17.29762, 275.14285, 3.65605
4given(0.08998, -0.7502, -0.65506), (-0.71592, 0.40852, -0.56619), (0.69236, 0.51991, -0.50033)109.82722, 86.63286, -71.66862
5given(0.04482, -0.66097, -0.74908), (0.72178, -0.49698, 0.48171), (-0.69067, -0.56226, 0.4548)97.93053, 202.59447, 82.52335
6given(-0.09227, 0.65699, 0.74823), (0.68151, 0.58952, -0.43359), (-0.72597, 0.46992, -0.50214)-87.55195, 54.53841, -58.03191
7given(-0.04694, 0.75114, 0.65847), (-0.68627, -0.50324, 0.52515), (0.72583, -0.42724, 0.53911)-100.50269, 210.04353, 56.85093
8given(0.09638, -0.71497, 0.69248), (-0.75325, 0.40239, 0.52029), (-0.65064, -0.57175, -0.49977)101.63394, 84.96857, 85.78767
9given(-0.0841, 0.6844, -0.72424), (0.65887, 0.58345, 0.47484), (0.74754, -0.43725, -0.49999)-87.80016, 53.33699, 60.50747
10given(-0.04463, -0.68886, 0.72352), (0.75852, -0.49468, -0.42419), (0.65012, 0.52987, 0.54459)98.61969, 204.12083, -75.21578
11given(0.03506, 0.72358, -0.68935), (-0.66056, -0.50083, -0.5593), (-0.74995, 0.47497, 0.46041)-93.85978, 212.22171, -60.92449

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Components

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


Mass: 18569.938 Da / Num. of mol.: 12 / Mutation: YES
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: Q9F5J9, UniProt: P0CB53*PLUS
#2: 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
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1502 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION GLN 8 TO GLY IN CHAINS A-L. ONLY THE CHAIN G MUTATION WAS VISIBLE IN THE ...ENGINEERED MUTATION GLN 8 TO GLY IN CHAINS A-L. ONLY THE CHAIN G MUTATION WAS VISIBLE IN THE ELECTRON DENSITY MAPS.
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: 2.3 Å3/Da / Density % sol: 46.6 %
Description: A 2.81A DATASET FOR THIS STRUCTURE WAS USED AS STARTING MODEL.
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8128
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: 0.8128 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 188319 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6 / Rsym value: 0.34 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE FROM PREVIOUS DATASET

Resolution: 1.81→19.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.178 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: LAST CYCLE OF REFINEMENT WAS DONE WITHOUT R-FREE SET. STATISTICS RELATED TO R-FREE ARE FORM SECOND LAST CYCLE. CRYSTAL SOAKED FOR 10 MIN IN 10 MM (NH4) 2FE(SO4)2 AND 2.5 PERCENT (SO2NA)2 I.E. REDUCTANT.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 9304 4.9 %RANDOM
Rwork0.187 ---
obs0.188 188314 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.4 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14499 0 73 1502 16074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9520906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.97451885
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.48225.26787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.619152679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5871565
X-RAY DIFFRACTIONr_chiral_restr0.0930.22290
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.28901
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.210819
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21584
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7941.59609
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.182215048
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.15436616
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2044.55858
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: 1.81→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 636
Rwork0.236 12917

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