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- PDB-4etr: X-ray structure of PA2169 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4etr
TitleX-ray structure of PA2169 from Pseudomonas aeruginosa
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / DUF2383 / domain of unknown function / cytoplasmic
Function / homology
Function and homology information


oxidoreductase activity / metal ion binding
Similarity search - Function
Conserved hypothetical protein CHP02284 / Uncharacterised conserved protein UCP029477 / Domain of unknown function DUF2383 / Domain of unknown function (DUF2383) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DUF2383 domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSchnell, R. / Sandalova, T. / Lindqvist, Y. / Schneider, G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: The AEROPATH project targeting Pseudomonas aeruginosa: crystallographic studies for assessment of potential targets in early-stage drug discovery.
Authors: Moynie, L. / Schnell, R. / McMahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / ...Authors: Moynie, L. / Schnell, R. / McMahon, S.A. / Sandalova, T. / Boulkerou, W.A. / Schmidberger, J.W. / Alphey, M. / Cukier, C. / Duthie, F. / Kopec, J. / Liu, H. / Jacewicz, A. / Hunter, W.N. / Naismith, J.H. / Schneider, G.
History
DepositionApr 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)34,3042
Polymers34,3042
Non-polymers00
Water37821
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,1521
Polymers17,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,1521
Polymers17,1521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.576, 71.219, 48.781
Angle α, β, γ (deg.)90.00, 111.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative uncharacterized protein


Mass: 17152.094 Da / Num. of mol.: 2 / Fragment: PA2169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2169 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I1U6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.91 Å3/Da / Density % sol: 35.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 19% PEG10K, 100 mM Na-acetate pH 4.6, SrCl2 20mM, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→45.36 Å / Num. all: 12342 / Num. obs: 11947 / % possible obs: 96.8 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.5 % / Biso Wilson estimate: 36.5 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 8.5
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1726 / Rsym value: 0.485 / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FSE, trimmed to the 4 helix module, side chains removed

3fse


Resolution: 2.25→45.35 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.665 / SU ML: 0.265 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): 2.6 / ESU R: 0.375 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28474 592 5 %RANDOM
Rwork0.22079 ---
all0.22381 12342 --
obs0.22381 11347 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.997 Å2
Baniso -1Baniso -2Baniso -3
1-5.93 Å20 Å23.1 Å2
2---2.77 Å20 Å2
3----0.88 Å2
Refine analyzeLuzzati coordinate error free: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.25→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1908 0 0 21 1929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211936
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9742608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.5524.643112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69815350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4551522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021504
X-RAY DIFFRACTIONr_mcbond_it0.8161.51212
X-RAY DIFFRACTIONr_mcangle_it1.56621916
X-RAY DIFFRACTIONr_scbond_it2.4953724
X-RAY DIFFRACTIONr_scangle_it4.2544.5692
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 37 -
Rwork0.375 837 -
obs-1726 96.15 %

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