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- PDB-8w1e: Crystal Structure of DPS-like protein PA4880 from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 8w1e
TitleCrystal Structure of DPS-like protein PA4880 from Pseudomonas aeruginosa (dodecamer)
ComponentsDPS-LIKE PROTEIN
KeywordsMETAL BINDING PROTEIN / PA4880 / DPS protein / metal binding / DNA cleavage / dodecamer
Function / homology
Function and homology information


ferroxidase / ferroxidase activity / ferric iron binding / iron ion transport / intracellular iron ion homeostasis / 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
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLovell, S. / Liu, L. / Seibold, 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
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
E: DPS-LIKE PROTEIN
F: DPS-LIKE PROTEIN
G: DPS-LIKE PROTEIN
H: DPS-LIKE PROTEIN
I: DPS-LIKE PROTEIN
J: DPS-LIKE PROTEIN
K: DPS-LIKE PROTEIN
L: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,41069
Polymers242,90012
Non-polymers4,51057
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 12 mer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)216.178, 216.178, 278.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
DPS-LIKE PROTEIN


Mass: 20241.627 Da / Num. of mol.: 12
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
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: 6.7 Å3/Da / Density % sol: 81.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Salt Rx F9: 800 mM lithium sulfate, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 24, 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: 2.9→49.51 Å / Num. obs: 145618 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.052 / Rrim(I) all: 0.198 / Χ2: 1 / Net I/σ(I): 12.8 / Num. measured all: 2082925
Reflection shellResolution: 2.9→2.95 Å / % possible obs: 100 % / Redundancy: 15.1 % / Rmerge(I) obs: 1.79 / Num. measured all: 107710 / Num. unique obs: 7128 / CC1/2: 0.711 / Rpim(I) all: 0.475 / Rrim(I) all: 1.852 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30.86 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 7326 5.04 %
Rwork0.1774 --
obs0.1786 145342 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→30.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16106 0 189 0 16295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00716454
X-RAY DIFFRACTIONf_angle_d0.88622248
X-RAY DIFFRACTIONf_dihedral_angle_d15.7496143
X-RAY DIFFRACTIONf_chiral_restr0.0412467
X-RAY DIFFRACTIONf_plane_restr0.0092973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.930.32380.29094552X-RAY DIFFRACTION100
2.93-2.970.31932440.27884565X-RAY DIFFRACTION100
2.97-30.29622670.27594512X-RAY DIFFRACTION100
3-3.040.33372390.27814560X-RAY DIFFRACTION100
3.04-3.080.30292350.28244566X-RAY DIFFRACTION100
3.08-3.120.27492660.28464514X-RAY DIFFRACTION100
3.12-3.170.37162360.31514529X-RAY DIFFRACTION100
3.17-3.220.32672450.2884553X-RAY DIFFRACTION100
3.22-3.270.3142510.24784559X-RAY DIFFRACTION100
3.27-3.320.28692480.23364560X-RAY DIFFRACTION100
3.32-3.380.28742580.24234525X-RAY DIFFRACTION100
3.38-3.440.2612270.2274590X-RAY DIFFRACTION100
3.44-3.50.25242660.22754535X-RAY DIFFRACTION100
3.5-3.580.26672420.21514567X-RAY DIFFRACTION100
3.58-3.650.20952440.18294563X-RAY DIFFRACTION100
3.65-3.740.19442410.1744578X-RAY DIFFRACTION100
3.74-3.830.19092420.16444591X-RAY DIFFRACTION100
3.83-3.930.1712160.15644606X-RAY DIFFRACTION100
3.93-4.050.16842360.15984585X-RAY DIFFRACTION100
4.05-4.180.17322420.14774610X-RAY DIFFRACTION100
4.18-4.330.16272500.14054590X-RAY DIFFRACTION100
4.33-4.50.15872620.13164617X-RAY DIFFRACTION100
4.5-4.710.15362160.12814629X-RAY DIFFRACTION100
4.71-4.950.15972510.14124596X-RAY DIFFRACTION100
4.95-5.260.15032500.14724659X-RAY DIFFRACTION100
5.26-5.670.19192480.17014633X-RAY DIFFRACTION100
5.67-6.230.23382220.1934689X-RAY DIFFRACTION100
6.23-7.120.16932330.16044717X-RAY DIFFRACTION100
7.12-8.940.12142580.1164747X-RAY DIFFRACTION100
8.94-30.860.15992530.15654919X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7712-0.4441-1.10570.52830.22671.5439-0.13120.0833-0.1087-0.09040.0361-0.0011-0.30990.0830.0990.593-0.0994-0.03870.3570.03260.519317.7276-42.8101-76.314
21.52230.04890.8950.615-0.08872.0785-0.12580.10890.1178-0.06080.0491-0.0977-0.0940.08710.08250.446-0.10980.07430.5315-0.02280.485829.5983-66.4816-88.3523
31.47470.02151.00040.9086-0.01153.4819-0.0524-0.037-0.0646-0.01530.0347-0.09640.380.24270.01560.4150.06710.07470.4312-0.07630.526433.8539-89.2917-75.8132
41.7786-0.2052-1.08630.75120.31752.4216-0.022-0.0532-0.1872-0.05610.0455-0.06530.24530.11960.0010.59350.02320.00770.2980.00540.509914.1422-103.3113-59.4226
51.42421.4415-0.45013.7038-0.60721.2589-0.0696-0.08290.06280.23620.08920.1017-0.12840.1385-0.01160.4380.0295-0.01890.3951-0.01450.329122.6256-66.3669-33.3288
62.3007-0.1421-0.80450.61130.07931.6422-0.0983-0.05530.00790.0736-0.02280.1728-0.34440.05490.10610.6133-0.0592-0.03540.3683-0.04260.520518.5098-42.7992-50.0677
71.46230.4952-0.00853.64390.38261.3498-0.18080.23710.0920.0080.1788-0.0316-0.2339-0.0929-0.01250.4125-0.0404-0.04190.44630.03140.33321.7747-61.4236-92.7578
80.76831.058-0.16733.3984-0.4051.3205-0.0885-0.013-0.1107-0.05030.1389-0.13250.22570.183-0.06090.40980.1095-0.02270.4740.02130.464233.9542-85.9972-46.5157
91.2573-0.43970.9230.7304-0.53491.9748-0.1029-0.10450.13670.1151-0.00240.0285-0.1477-0.0880.09280.57030.08230.07570.4633-0.06720.5438-4.0906-56.1662-38.0457
100.69760.64330.3253.36540.54121.3986-0.03110.0386-0.0210.05840.07130.07650.0846-0.1987-0.0370.3502-0.0134-0.03480.5874-0.01590.4978-18.0259-71.6689-79.1899
111.7199-0.0492-0.89810.74870.0742.38160.04470.0325-0.15250.0258-0.03660.11550.1041-0.32150.0240.4968-0.14720.01850.4126-0.01920.521-10.2357-96.4418-65.8301
121.1521-0.28691.09460.9178-0.48082.90190.03140.02880.01940.002-0.07550.1320.1741-0.38730.03530.3935-0.02290.10090.5889-0.00970.5522-19.4095-73.8601-49.7098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 9 through 176)
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 176)
3X-RAY DIFFRACTION3(chain 'C' and resid 10 through 177)
4X-RAY DIFFRACTION4(chain 'D' and resid 8 through 177)
5X-RAY DIFFRACTION5(chain 'E' and resid 8 through 177)
6X-RAY DIFFRACTION6(chain 'F' and resid 8 through 176)
7X-RAY DIFFRACTION7(chain 'G' and resid 9 through 177)
8X-RAY DIFFRACTION8(chain 'H' and resid 9 through 177)
9X-RAY DIFFRACTION9(chain 'I' and resid 8 through 177)
10X-RAY DIFFRACTION10(chain 'J' and resid 9 through 177)
11X-RAY DIFFRACTION11(chain 'K' and resid 8 through 177)
12X-RAY DIFFRACTION12(chain 'L' and resid 10 through 177)

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