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- PDB-2d5k: Crystal structure of Dps from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 2d5k
TitleCrystal structure of Dps from Staphylococcus aureus
ComponentsDps family protein
KeywordsMETAL BINDING PROTEIN / FOUR HELIX BUNDLE
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis
Similarity search - Function
Dps protein family signature 1. / DNA-binding protein Dps, conserved site / 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
Dps family protein / Dps family protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTanaka, Y. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: FEMS Microbiol. Lett. / Year: 2014
Title: Nucleoid compaction by MrgA(Asp56Ala/Glu60Ala) does not contribute to staphylococcal cell survival against oxidative stress and phagocytic killing by macrophages
Authors: Ushijima, Y. / Ohniwa, R.L. / Maruyama, A. / Saito, S. / Tanaka, Y. / Morikawa, K.
History
DepositionNov 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 family protein
B: Dps family protein
C: Dps family protein
D: Dps family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5756
Polymers71,3914
Non-polymers1842
Water9,260514
1
A: Dps family protein
B: Dps family protein
C: Dps family protein
D: Dps family protein
hetero molecules

A: Dps family protein
B: Dps family protein
C: Dps family protein
D: Dps family protein
hetero molecules

A: Dps family protein
B: Dps family protein
C: Dps family protein
D: Dps family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,72618
Polymers214,17312
Non-polymers5536
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area34930 Å2
ΔGint-204 kcal/mol
Surface area61910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)143.381, 143.381, 88.288
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThe biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operateions: -y, x-y+1, z and -x+y-1, -x, z.

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Components

#1: Protein
Dps family protein / Dps


Mass: 17847.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: COL / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q5HE61, UniProt: A0A0H2X069*PLUS, dihydrodipicolinate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M MgCl2, 0.1M Tris, 10% PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 89128 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 19.2 Å2 / Rsym value: 0.064
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 10.6 % / Num. unique all: 8804 / Rsym value: 0.28 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JI5

1ji5


Resolution: 1.85→9.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2323007.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 8810 10 %RANDOM
Rwork0.19 ---
obs0.19 88504 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 72.795 Å2 / ksol: 0.503825 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å20.2 Å20 Å2
2---1.87 Å20 Å2
3---3.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.85→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 12 514 5239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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: 1.85→1.97 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 1443 9.9 %
Rwork0.207 13166 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein_rep.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3gol_xplor_2.paramgol_xplor_2.top

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