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- PDB-8ff9: Crystal structure of Apo Dps protein (PA0962) from Pseudomonas ae... -

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Basic information

Entry
Database: PDB / ID: 8ff9
TitleCrystal structure of Apo Dps protein (PA0962) from Pseudomonas aeruginosa (orthorhombic form)
ComponentsProbable dna-binding stress protein
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Probable dna-binding stress protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rivera, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI169344 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: Int J Mol Sci / Year: 2023
Title: Pseudomonas aeruginosa Dps (PA0962) Functions in H 2 O 2 Mediated Oxidative Stress Defense and Exhibits In Vitro DNA Cleaving Activity.
Authors: Rajapaksha, N. / Soldano, A. / Yao, H. / Donnarumma, F. / Kashipathy, M.M. / Seibold, S. / Battaile, K.P. / Lovell, S. / Rivera, M.
History
DepositionDec 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable dna-binding stress protein
B: Probable dna-binding stress protein
C: Probable dna-binding stress protein
D: Probable dna-binding stress protein
E: Probable dna-binding stress protein
F: Probable dna-binding stress protein
G: Probable dna-binding stress protein
H: Probable dna-binding stress protein
I: Probable dna-binding stress protein
J: Probable dna-binding stress protein
K: Probable dna-binding stress protein
L: Probable dna-binding stress protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,039129
Polymers210,13112
Non-polymers8,908117
Water41,8492323
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.541, 129.820, 156.598
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable dna-binding stress protein


Mass: 17510.916 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA0962 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9I4Z7
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 81 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.13 Å3/Da / Density % sol: 60.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1 M (NH4)2SO4, 1M KCl, 100 mM HEPES

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Aug 1, 2020
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→48.43 Å / Num. obs: 288462 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Χ2: 1.02 / Net I/σ(I): 10.8 / Num. measured all: 1964310
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.159 / Num. measured all: 98554 / Num. unique obs: 14185 / CC1/2: 0.632 / Rpim(I) all: 0.469 / Rrim(I) all: 1.252 / Χ2: 1.06 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIXdev_3959refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.43 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 16.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1695 14417 5 %
Rwork0.1461 --
obs0.1473 288307 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14587 0 441 2323 17351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915298
X-RAY DIFFRACTIONf_angle_d0.94620863
X-RAY DIFFRACTIONf_dihedral_angle_d12.2335515
X-RAY DIFFRACTIONf_chiral_restr0.0512354
X-RAY DIFFRACTIONf_plane_restr0.012644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.27585010.23999030X-RAY DIFFRACTION100
1.72-1.740.26894440.22949073X-RAY DIFFRACTION100
1.74-1.760.25044550.21969105X-RAY DIFFRACTION100
1.76-1.780.22884940.20629039X-RAY DIFFRACTION100
1.78-1.810.22954740.2039034X-RAY DIFFRACTION100
1.81-1.830.23474900.19259090X-RAY DIFFRACTION100
1.83-1.860.21624680.1829045X-RAY DIFFRACTION100
1.86-1.890.21224450.18329121X-RAY DIFFRACTION100
1.89-1.910.21144700.17649072X-RAY DIFFRACTION100
1.91-1.950.19814650.17279031X-RAY DIFFRACTION100
1.95-1.980.20134890.17399080X-RAY DIFFRACTION100
1.98-2.020.1984540.16249140X-RAY DIFFRACTION100
2.02-2.050.18344950.15349070X-RAY DIFFRACTION100
2.05-2.10.17624930.14029081X-RAY DIFFRACTION100
2.1-2.140.17364750.13329056X-RAY DIFFRACTION100
2.14-2.190.17544760.13529119X-RAY DIFFRACTION100
2.19-2.250.15524890.12989080X-RAY DIFFRACTION100
2.25-2.310.16354590.12129127X-RAY DIFFRACTION100
2.31-2.380.15524710.12649118X-RAY DIFFRACTION100
2.38-2.450.14734840.12589145X-RAY DIFFRACTION100
2.45-2.540.18575280.14279087X-RAY DIFFRACTION100
2.54-2.640.17994670.14199144X-RAY DIFFRACTION100
2.64-2.760.16694960.14529101X-RAY DIFFRACTION100
2.76-2.910.18245220.15749141X-RAY DIFFRACTION100
2.91-3.090.18324830.16549187X-RAY DIFFRACTION100
3.09-3.330.16584450.14789234X-RAY DIFFRACTION100
3.33-3.660.14174360.13069233X-RAY DIFFRACTION100
3.66-4.190.12135250.10919226X-RAY DIFFRACTION100
4.19-5.280.14115360.11859257X-RAY DIFFRACTION100
5.28-48.430.17364880.16669624X-RAY DIFFRACTION100

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