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

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Basic information

Entry
Database: PDB / ID: 8ffa
TitleCrystal structure of Apo Dps protein (PA0962) from Pseudomonas aeruginosa (cubic 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 PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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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
M: Probable dna-binding stress protein
N: Probable dna-binding stress protein
O: Probable dna-binding stress protein
P: Probable dna-binding stress protein


Theoretical massNumber of molelcules
Total (without water)280,17516
Polymers280,17516
Non-polymers00
Water20,9511163
1
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


Theoretical massNumber of molelcules
Total (without water)210,13112
Polymers210,13112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42200 Å2
ΔGint-201 kcal/mol
Surface area57970 Å2
MethodPISA
2
M: Probable dna-binding stress protein
N: Probable dna-binding stress protein
O: Probable dna-binding stress protein
P: Probable dna-binding stress protein

M: Probable dna-binding stress protein
N: Probable dna-binding stress protein
O: Probable dna-binding stress protein
P: Probable dna-binding stress protein

M: Probable dna-binding stress protein
N: Probable dna-binding stress protein
O: Probable dna-binding stress protein
P: Probable dna-binding stress protein


Theoretical massNumber of molelcules
Total (without water)210,13112
Polymers210,13112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x+1/2,-y+1/21
crystal symmetry operation11_455y-1/2,-z+1/2,-x1
Buried area42060 Å2
ΔGint-198 kcal/mol
Surface area58150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.465, 223.465, 223.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11M-275-

HOH

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Components

#1: Protein
Probable dna-binding stress protein


Mass: 17510.916 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA0962 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q9I4Z7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M sodium malonate, 100 mM Hepes, 0.5% (v/v) Jeffamine ED-2001

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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: Jun 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: 2.15→49.97 Å / Num. obs: 200207 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.045 / Rrim(I) all: 0.207 / Χ2: 1 / Net I/σ(I): 12.5 / Num. measured all: 4163876
Reflection shellResolution: 2.15→2.19 Å / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 2.343 / Num. measured all: 210869 / Num. unique obs: 9858 / CC1/2: 0.612 / Rpim(I) all: 0.518 / Rrim(I) all: 2.4 / Χ2: 0.99 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4043refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→49.97 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 24.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 10047 5.02 %
Rwork0.1829 --
obs0.1852 200109 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→49.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19175 0 0 1163 20338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01119543
X-RAY DIFFRACTIONf_angle_d1.0526573
X-RAY DIFFRACTIONf_dihedral_angle_d13.7857057
X-RAY DIFFRACTIONf_chiral_restr0.0543088
X-RAY DIFFRACTIONf_plane_restr0.0123430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.29583090.25376351X-RAY DIFFRACTION100
2.17-2.20.3123320.25376235X-RAY DIFFRACTION100
2.2-2.230.29633350.24336275X-RAY DIFFRACTION100
2.23-2.250.2952960.23576326X-RAY DIFFRACTION100
2.26-2.280.2833210.22876351X-RAY DIFFRACTION100
2.28-2.320.27843460.22556243X-RAY DIFFRACTION100
2.32-2.350.28642770.21846436X-RAY DIFFRACTION100
2.35-2.380.2483330.21646257X-RAY DIFFRACTION100
2.38-2.420.25163250.20426302X-RAY DIFFRACTION100
2.42-2.460.26643780.21056299X-RAY DIFFRACTION100
2.46-2.50.27633180.21426284X-RAY DIFFRACTION100
2.5-2.550.2713760.21076338X-RAY DIFFRACTION100
2.55-2.60.27053360.20976256X-RAY DIFFRACTION100
2.6-2.650.26062850.20636351X-RAY DIFFRACTION100
2.65-2.710.28253570.23066281X-RAY DIFFRACTION100
2.71-2.770.26873600.21686307X-RAY DIFFRACTION100
2.77-2.840.25563730.20766245X-RAY DIFFRACTION100
2.84-2.920.26563750.2036304X-RAY DIFFRACTION100
2.92-30.26043170.20776319X-RAY DIFFRACTION100
3-3.10.25163210.20866391X-RAY DIFFRACTION100
3.1-3.210.27063100.20436328X-RAY DIFFRACTION100
3.21-3.340.25533510.20476327X-RAY DIFFRACTION100
3.34-3.490.23283280.1836355X-RAY DIFFRACTION100
3.49-3.680.2143770.16986327X-RAY DIFFRACTION100
3.68-3.910.19053050.1566402X-RAY DIFFRACTION100
3.91-4.210.1743480.13656357X-RAY DIFFRACTION100
4.21-4.630.16883270.13216398X-RAY DIFFRACTION100
4.63-5.30.18213160.13846426X-RAY DIFFRACTION100
5.3-6.670.22153650.1866423X-RAY DIFFRACTION100
6.68-49.970.18613500.16736568X-RAY DIFFRACTION99

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