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- PDB-1yx1: Crystal Structure of Protein of Unknown Function PA2260 from Pseu... -

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Basic information

Entry
Database: PDB / ID: 1yx1
TitleCrystal Structure of Protein of Unknown Function PA2260 from Pseudomonas aeruginosa, Possible Sugar Phosphate Isomerase
Componentshypothetical protein PA2260
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / PA2260 / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDivalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / ISOPROPYL ALCOHOL / AP endonuclease
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsOsipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of hypothetical protein PA2260 from Pseudomonas aeruginosa
Authors: Osipiuk, J. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionFeb 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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 protein PA2260
B: hypothetical protein PA2260
C: hypothetical protein PA2260
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6857
Polymers88,4823
Non-polymers2034
Water12,268681
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.636, 91.913, 124.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein PA2260


Mass: 29494.018 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Gene: PA2260 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I1L3
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M Bis_Tris pH 6.5, 8% PEG 5000 MME, 4% isopropyl alcohol, 50 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97943 / Wavelength: 0.97943 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 26, 2004
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. all: 80010 / Num. obs: 75770 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 34.5
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.32 / % possible all: 59.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 3.281 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2019 2258 -RANDOM
Rwork0.16947 ---
obs0.16947 75767 86.21 %-
all-75767 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.331 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2--1.44 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 13 681 6584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9778437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8065748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03322.539323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0211587
X-RAY DIFFRACTIONr_chiral_restr0.1090.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024792
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.22986
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.24181
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2587
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9321.53771
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64126042
X-RAY DIFFRACTIONr_scbond_it2.82432542
X-RAY DIFFRACTIONr_scangle_it4.554.52395
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.795→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.207 2491 -
Rfree-0 -
obs--38.73 %
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)
10.5057-0.24760.14780.4485-0.19910.68840.02710.0437-0.03160.02210.0104-0.01860.0409-0.0201-0.0375-0.0264-0.0019-0.0253-0.036-0.0022-0.019526.103111.218853.7481
20.8939-0.2304-0.11610.5944-0.02240.7530.05910.00820.0384-0.058-0.0220.0226-0.0752-0.0168-0.037-0.01960.01390.0071-0.03870.0088-0.04163.233439.932739.1471
30.2111-0.0271-0.28490.639-0.10331.2827-0.0010.001-0.0098-0.0512-0.0026-0.0489-0.13410.17670.0036-0.0148-0.04480.0116-0.00430.0032-0.049532.597124.240316.4888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 2525 - 254
2X-RAY DIFFRACTION2BB3 - 2535 - 255
3X-RAY DIFFRACTION3CC3 - 2525 - 254

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