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- PDB-1u6l: Crystal structure of protein PA1353 from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 1u6l
TitleCrystal structure of protein PA1353 from Pseudomonas aeruginosa
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / hypothetical protein / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyPhnB-like / 3-demethylubiquinone-9 3-methyltransferase / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta / 3-dmu-9_3-mt domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å
AuthorsMin, T. / Mu, H. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of a hypothetical protein from Pseudomonas aeruginosa
Authors: Min, T. / Mu, H. / Shapiro, L.
History
DepositionJul 30, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)33,5742
Polymers33,5742
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-32 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.579, 76.294, 82.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsNot known

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Components

#1: Protein hypothetical protein


Mass: 16786.818 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I3Z1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.78 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG 6000, 1M Lithium Chloride, 0.1M sodium Acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 24, 2004
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 9121 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.111
Reflection shellHighest resolution: 2.8 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.81→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 7.668 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.599 / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25712 434 4.8 %RANDOM
Rwork0.19709 ---
obs0.1999 9085 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.815 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---0.98 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.81→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1985 0 0 243 2228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0222039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5331.942763
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8685262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17123.57184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.73315293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.335158
X-RAY DIFFRACTIONr_chiral_restr0.1550.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021574
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2890.21106
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.350.21396
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2690.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4110.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3740.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it5.0431.51360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.17822087
X-RAY DIFFRACTIONr_scbond_it5.9233816
X-RAY DIFFRACTIONr_scangle_it8.5994.5696
X-RAY DIFFRACTIONr_rigid_bond_restr4.78932176
X-RAY DIFFRACTIONr_sphericity_free8.6923279
X-RAY DIFFRACTIONr_sphericity_bonded5.14831996
LS refinement shellResolution: 2.81→2.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.672 32 -
Rwork0.364 601 -
obs--98.29 %

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