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- PDB-2x3o: Crystal Structure of the Hypothetical Protein PA0856 from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2x3o
TitleCrystal Structure of the Hypothetical Protein PA0856 from Pseudomonas aeruginosa
ComponentsHYPOTHETICAL PROTEIN PA0856Hypothesis
KeywordsUNKNOWN FUNCTION
Function / homologyDomain of unknown function DUF2059 / Uncharacterized protein conserved in bacteria (DUF2059) / DUF2059 domain-containing protein
Function and homology information
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionJan 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN PA0856
B: HYPOTHETICAL PROTEIN PA0856
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7074
Polymers33,5792
Non-polymers1282
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-58.1 kcal/mol
Surface area16280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.440, 51.740, 68.800
Angle α, β, γ (deg.)90.00, 102.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HYPOTHETICAL PROTEIN PA0856 / Hypothesis


Mass: 16789.639 Da / Num. of mol.: 2 / Fragment: RESIDUES 35-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9I585
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FINAL CONSTRUCT ENTERING CRYSTALLIZATION TRIALS WAS A TRUNCATED VERSION (RESIDUES 1-36 REMOVED) ...THE FINAL CONSTRUCT ENTERING CRYSTALLIZATION TRIALS WAS A TRUNCATED VERSION (RESIDUES 1-36 REMOVED) BECAUSE THIS REGION WAS PREDICTED TO CODE FOR A SIGNAL PEPTIDE.

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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: 3.86 Å3/Da / Density % sol: 68.1 % / Description: NONE
Crystal growpH: 6.5
Details: 36.3% PEGMME 550, 0.1M SODIUM CACODYLATE PH 6.5, 0.16M DI-AMMONIUM PHOSPHATE. CRYSTALS WERE CRYOPROTECTED WITH 3.67% HEXANEDIOL IN THE ABOVE SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.9→29.14 Å / Num. obs: 10798 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.97
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.22 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→29.14 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU B: 18.571 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R: 0.766 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31584 544 4.8 %RANDOM
Rwork0.26205 ---
obs0.26472 10798 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-1.27 Å2
2---1.02 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2132 0 7 12 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9872919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4645268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41226.2596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.10515426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.836158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211584
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6561.51354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27222168
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1453815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4624.5751
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.902→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 35 -
Rwork0.293 782 -
obs--98.91 %

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