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- PDB-1sh8: 1.5 A Crystal Structure of a Protein of Unknown Function PA5026 f... -

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Basic information

Entry
Database: PDB / ID: 1sh8
Title1.5 A Crystal Structure of a Protein of Unknown Function PA5026 from Pseudomonas aeruginosa, Probable Thioesterase
Componentshypothetical protein PA5026
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Pseudomonas aeruginosa / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF4442 / Domain of unknown function (DUF4442) / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta / DUF4442 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsZhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.5A crystal structure of a hypothetical protein PA5026 from Pseudomonas aeruginosa
Authors: Zhang, R. / Evdokimova, E. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionFeb 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PA5026
B: hypothetical protein PA5026


Theoretical massNumber of molelcules
Total (without water)34,2972
Polymers34,2972
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-15 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.608, 72.231, 91.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThis protein exists as dimer. Mol.A and Mol.B represents the dimer in asymetric unit.

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Components

#1: Protein hypothetical protein PA5026


Mass: 17148.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA5026 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
Keywords: a few residues of histag plus protein plus 2 extra residues at C-terminal in mol.A
References: UniProt: Q9HUE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.8 Å3/Da / Density % sol: 55.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: NaForm 2M, 0.1M NaAcet. 2%MPD, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795,0.9797,0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Feb 8, 2004 / Details: morrors
RadiationMonochromator: Si 111 channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97971
30.946561
ReflectionResolution: 1.5→50 Å / Num. all: 115037 / Num. obs: 109285 / % possible obs: 95 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 4.97 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.25
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.98 / Num. unique all: 11501 / % possible all: 64.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→23.24 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 259680.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5142 4.9 %RANDOM
Rwork0.197 ---
obs0.197 104611 90.7 %-
all-115337 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.3313 Å2 / ksol: 0.369007 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--1.48 Å20 Å2
3----2.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→23.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2374 0 0 332 2706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 583 5 %
Rwork0.271 11031 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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