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- PDB-8w1d: CRYSTAL STRUCTURE OF DPS-LIKE PROTEIN PA4880 FROM PSEUDOMONAS AER... -

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Basic information

Entry
Database: PDB / ID: 8w1d
TitleCRYSTAL STRUCTURE OF DPS-LIKE PROTEIN PA4880 FROM PSEUDOMONAS AERUGINOSA (DIMERIC FORM)
ComponentsDPS-LIKE PROTEIN
KeywordsMETAL BINDING PROTEIN / PA4880 / DPS protein / metal binding / DNA cleavage
Function / homology
Function and homology information


intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion transport / iron ion binding / heme binding / cytosol
Similarity search - Function
DNA-binding protein from starved cells-like / Bacterioferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Bacterioferritin
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsLovell, S. / Battaile, K.P. / Rivera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI169344 United States
CitationJournal: Front Mol Biosci / Year: 2024
Title: Pseudomonas aeruginosa gene PA4880 encodes a Dps-like protein with a Dps fold, bacterioferritin-type ferroxidase centers, and endonuclease activity.
Authors: Rajapaksha, N. / Yao, H. / Cook, A. / Seibold, S. / Liu, L. / Battaile, K.P. / Fontenot, L. / Donnarumma, F. / Lovell, S. / Rivera, M.
History
DepositionFeb 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3533
Polymers20,2421
Non-polymers1122
Water2,648147
1
A: DPS-LIKE PROTEIN
hetero molecules

A: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7076
Polymers40,4832
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area2850 Å2
ΔGint-73 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.938, 44.580, 51.468
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DPS-LIKE PROTEIN


Mass: 20241.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4880 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HUT3
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.63 Å3/Da / Density % sol: 24.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Proplex D5: 8% (w/v) PEG 6,000, 100 mM MES pH 6.0, 100 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 14, 2020
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.3→28.76 Å / Num. obs: 32140 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.027 / Rrim(I) all: 0.088 / Χ2: 0.91 / Net I/σ(I): 12.3 / Num. measured all: 327050
Reflection shellResolution: 1.3→1.32 Å / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 1.18 / Num. measured all: 13991 / Num. unique obs: 1585 / CC1/2: 0.824 / Rpim(I) all: 0.419 / Rrim(I) all: 1.253 / Χ2: 0.76 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX(1.18rc4_3812: ???)refinement
Aimlessdata scaling
XDSdata reduction
SHELXCDphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.3→28.76 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 19.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.179 1559 4.86 %
Rwork0.1451 --
obs0.1468 32096 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 2 147 1320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071193
X-RAY DIFFRACTIONf_angle_d0.9221614
X-RAY DIFFRACTIONf_dihedral_angle_d14.936450
X-RAY DIFFRACTIONf_chiral_restr0.056182
X-RAY DIFFRACTIONf_plane_restr0.006216
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.26741240.21762758X-RAY DIFFRACTION100
1.34-1.390.22061600.18822737X-RAY DIFFRACTION100
1.39-1.450.19271470.16582752X-RAY DIFFRACTION100
1.45-1.510.18071490.13312765X-RAY DIFFRACTION100
1.51-1.590.18121300.11722773X-RAY DIFFRACTION100
1.59-1.690.17871320.11952764X-RAY DIFFRACTION100
1.69-1.820.18191520.12672782X-RAY DIFFRACTION100
1.82-20.16661390.12782773X-RAY DIFFRACTION100
2-2.290.15881400.12562785X-RAY DIFFRACTION100
2.29-2.890.16491390.15112796X-RAY DIFFRACTION100
2.89-28.760.18611470.15532852X-RAY DIFFRACTION100

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