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- PDB-1y0n: Structure of Protein of Unknown Function PA3463 from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 1y0n
TitleStructure of Protein of Unknown Function PA3463 from Pseudomonas aeruginosa PAO1
ComponentsHypothetical UPF0270 protein PA3463
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / MCSG / Midwest Center for Structural Genomics / Protein Structure Initiative / PSI / Pseudomonsa aeruginosa / hypothetical protein
Function / homologyYehU-like / Uncharacterised protein family UPF0270 / YehU-like superfamily / Uncharacterised protein family (UPF0270) / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / UPF0270 protein PA3463
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBinkowski, T.A. / Edwards, A. / Savchenko, A. / Skarina, T. / Gorodichtchenskaia, E. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Hypothetical protein PA3463 from Pseudomonas aeruginosa strain PAO1
Authors: Binkowski, T.A. / Edwards, A. / Savchenko, A. / Skarina, T. / Gorodichtchenskaia, E. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0270 protein PA3463
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2715
Polymers8,9031
Non-polymers3684
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.311, 78.311, 52.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-102-

GOL

21A-102-

GOL

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Components

#1: Protein Hypothetical UPF0270 protein PA3463


Mass: 8902.952 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA3463 / Plasmid: PET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYE3
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: Na Citrate 1.4M, 0.1M Hepes Na, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jul 21, 2004
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→28.51 Å / Num. obs: 6791
Reflection shellResolution: 2.002→2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→28.51 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.785 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28893 322 4.8 %RANDOM
Rwork0.24565 ---
all0.24761 6688 --
obs0.24761 6366 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→28.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 0 24 28 626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0752.019805
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.919569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13323.43832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11715106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.833158
X-RAY DIFFRACTIONr_chiral_restr0.140.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02440
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2690.2247
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.2389
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3230.233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6890.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5090.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.5941.5370
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6222573
X-RAY DIFFRACTIONr_scbond_it3.9223248
X-RAY DIFFRACTIONr_scangle_it5.6074.5232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 21 -
Rwork0.399 404 -
obs--88.91 %

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