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- PDB-8ffd: Crystal structure of manganeese bound Dps protein (PA0962) from P... -

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Basic information

Entry
Database: PDB / ID: 8ffd
TitleCrystal structure of manganeese bound 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
: / L(+)-TARTARIC ACID / Probable dna-binding stress protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLovell, S. / Seibold, S. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,35434
Polymers280,17516
Non-polymers1,17918
Water37,8502101
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,09026
Polymers210,13112
Non-polymers95914
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45010 Å2
ΔGint-258 kcal/mol
Surface area57440 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
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)210,79024
Polymers210,13112
Non-polymers65912
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area44350 Å2
ΔGint-251 kcal/mol
Surface area57710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.914, 223.914, 223.914
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-390-

HOH

21M-458-

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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2101 / 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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.8 M Na/K tartrate, 100 mM Tris, 0.5% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 291 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Jun 6, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→48.86 Å / Num. obs: 188113 / % possible obs: 100 % / Redundancy: 10.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.061 / Rrim(I) all: 0.198 / Χ2: 1.01 / Net I/σ(I): 10.2 / Num. measured all: 1964631
Reflection shellResolution: 2.2→2.24 Å / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.272 / Num. measured all: 87882 / Num. unique obs: 9297 / CC1/2: 0.638 / Rpim(I) all: 0.436 / Rrim(I) all: 1.346 / Χ2: 1 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→48.86 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 23.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 9437 5.02 %
Rwork0.1696 --
obs0.1723 188052 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→48.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19312 0 36 2101 21449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919922
X-RAY DIFFRACTIONf_angle_d0.96227122
X-RAY DIFFRACTIONf_dihedral_angle_d13.5087314
X-RAY DIFFRACTIONf_chiral_restr0.0483142
X-RAY DIFFRACTIONf_plane_restr0.013516
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.3413330.2545906X-RAY DIFFRACTION100
2.23-2.250.29463090.23635920X-RAY DIFFRACTION100
2.25-2.280.28513600.22835892X-RAY DIFFRACTION100
2.28-2.310.30133500.22565895X-RAY DIFFRACTION100
2.31-2.340.29343420.21845848X-RAY DIFFRACTION100
2.34-2.370.27412940.20555908X-RAY DIFFRACTION100
2.37-2.40.25142720.19625995X-RAY DIFFRACTION100
2.4-2.440.28333170.19795933X-RAY DIFFRACTION100
2.44-2.480.26742990.20355894X-RAY DIFFRACTION100
2.48-2.520.2753080.20085973X-RAY DIFFRACTION100
2.52-2.560.25262940.19575919X-RAY DIFFRACTION100
2.56-2.610.26062910.19525985X-RAY DIFFRACTION100
2.61-2.660.2753090.19235899X-RAY DIFFRACTION100
2.66-2.710.25773090.19445915X-RAY DIFFRACTION100
2.71-2.770.24922950.18485969X-RAY DIFFRACTION100
2.77-2.840.23353510.17845878X-RAY DIFFRACTION100
2.84-2.910.23413480.17435915X-RAY DIFFRACTION100
2.91-2.990.21812970.17555989X-RAY DIFFRACTION100
2.99-3.070.24043430.18495881X-RAY DIFFRACTION100
3.07-3.170.22542770.17735990X-RAY DIFFRACTION100
3.17-3.290.24713060.17635963X-RAY DIFFRACTION100
3.29-3.420.22873260.16245907X-RAY DIFFRACTION100
3.42-3.570.23583110.15855964X-RAY DIFFRACTION100
3.57-3.760.21383090.14666001X-RAY DIFFRACTION100
3.76-40.18393380.13695968X-RAY DIFFRACTION100
4-4.310.16732810.12276019X-RAY DIFFRACTION100
4.31-4.740.16563020.12126002X-RAY DIFFRACTION100
4.74-5.420.16773410.13455998X-RAY DIFFRACTION100
5.42-6.830.21843220.18026057X-RAY DIFFRACTION100
6.83-48.860.18583030.17316232X-RAY DIFFRACTION100

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