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- PDB-2cf7: Asp74Ala mutant crystal structure for Dps-like peroxide resistanc... -

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Basic information

Entry
Database: PDB / ID: 2cf7
TitleAsp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis.
ComponentsDPR
KeywordsPEROXIDE RESISTANCE / DPS-FAMILY / FERRITIN-LIKE / FERROXIDASE / IRON-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: 1.5 Å
AuthorsKauko, A. / Pulliainen, A.T. / 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
DepositionFeb 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 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: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / 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 / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DPR
B: DPR
C: DPR
D: DPR
E: DPR
F: DPR
G: DPR
H: DPR
I: DPR
J: DPR
K: DPR
L: DPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,45521
Polymers222,31112
Non-polymers1,1449
Water36,8952048
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.930, 133.670, 135.630
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(0.99887, -0.04383, -0.01817), (-0.04384, -0.99904, -0.00011), (-0.01815, 0.00091, -0.99983)7.01819, 268.59369, 134.30066
2given(-0.99992, 0.01002, -0.00757), (0.00725, -0.03192, -0.99946), (-0.01025, -0.99944, 0.03185)97.83053, 203.83597, 198.22627
3given(-0.99886, 0.02002, 0.0433), (0.04386, 0.02825, 0.99864), (0.01877, 0.9994, -0.0291)93.44682, 60.7854, -65.28944
4given(-0.0189, 0.68523, -0.72808), (-0.73487, -0.5033, -0.4546), (-0.67795, 0.52645, 0.51307)7.37131, 267.04788, -4.16797
5given(-0.02125, -0.69552, 0.71819), (-0.70743, 0.51807, 0.48078), (-0.70647, -0.49785, -0.50304)94.82462, 67.43401, 201.27153
6given(0.02778, 0.70162, -0.71201), (0.73382, 0.46936, 0.49114), (0.67878, -0.53613, -0.50182)1.79706, 1.79991, 138.26321
7given(0.01357, -0.70748, 0.7066), (0.70847, -0.49187, -0.5061), (0.70561, 0.50747, 0.49455)95.4881, 197.52802, -68.43137
8given(-0.01567, -0.72888, -0.68446), (0.69121, -0.50253, 0.51932), (-0.72248, -0.46497, 0.51169)192.45802, 131.34935, 130.13071
9given(0.03659, 0.73011, 0.68235), (0.69578, 0.47151, -0.54182), (-0.71733, 0.49459, -0.49074)-95.39014, 72.24183, 69.1798
10given(0.01995, 0.69853, 0.7153), (-0.69741, -0.50292, 0.51058), (0.7164, -0.50904, 0.47713)-92.43738, 200.57164, 67.19962
11given(-0.03773, -0.70127, -0.71189), (-0.68839, 0.53464, -0.49018), (0.72435, 0.47157, -0.50293)191.83812, 128.79024, 1.7741

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Components

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


Mass: 18525.928 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-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 2048 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 74 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN E, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN F, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN G, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN H, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN I, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN J, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN K, ASP 74 TO ALA ENGINEERED RESIDUE IN CHAIN L, ASP 74 TO ALA
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. THIS PROTEIN HAS ALSO D74A 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 %
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 MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8128 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 308623 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 22.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMN

1umn


Resolution: 1.5→19.28 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.763 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ONE ROUND OF REFINEMENT WITH ALL DATA WAS RUN AFTER THE WORKING AND TEST SETS WERE MERGED.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 14747 4.8 %RANDOM
Rwork0.153 ---
obs0.154 308607 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.25 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14367 0 65 2048 16480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215483
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.95221146
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64152017
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.60825.112761
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.155152688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4121561
X-RAY DIFFRACTIONr_chiral_restr0.0950.22332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.28648
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.210988
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.21837
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9761.59545
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.449215131
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42536677
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7774.55903
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.207 1125
Rwork0.154 22512

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