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- PDB-1s7i: 1.8 A Crystal Structure of a Protein of Unknown Function PA1349 f... -

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Basic information

Entry
Database: PDB / ID: 1s7i
Title1.8 A Crystal Structure of a Protein of Unknown Function PA1349 from Pseudomonas aeruginosa
Componentshypothetical protein PA1349
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / protein structure initiative / Pseudomonas aeruginosa / MCSG / PSI / Midwest Center for Structural Genomics
Function / homologyYCII-related / YCII-related domain / Dimeric alpha+beta barrel / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / YCII-related domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsZhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.8A crystal structure of a hypothetical protein PA1349 from Pseudomonas aeruginosa
Authors: Zhang, R. / Skarina, T. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 PA1349


Theoretical massNumber of molelcules
Total (without water)13,6341
Polymers13,6341
Non-polymers00
Water1,02757
1
A: hypothetical protein PA1349

A: hypothetical protein PA1349


Theoretical massNumber of molelcules
Total (without water)27,2672
Polymers27,2672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_454-z-1/4,-y+3/4,-x-1/41
Buried area4050 Å2
ΔGint-24 kcal/mol
Surface area13550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.437, 103.437, 103.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
DetailsThis protein existed as dimer. The second part of the biological assembly is generated by the crystallographic two fold axis

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Components

#1: Protein hypothetical protein PA1349


Mass: 13633.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA1349 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I3Z5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.44 Å3/Da / Density % sol: 63.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M Amm. Sulph., 0.1M Tris, pH 8.5, 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: Dec 11, 2003 / Details: mirrors
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: 1.8→50 Å / Num. all: 18121 / Num. obs: 17179 / % possible obs: 94.8 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4 / Redundancy: 9.12 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 41.33
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.71 / Num. unique all: 1759 / % possible all: 76.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→28.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 827357.77 / 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
Rfree0.262 1503 5 %RANDOM
Rwork0.218 ---
obs0.218 29975 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.9607 Å2 / ksol: 0.376487 e/Å3
Displacement parametersBiso mean: 33.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 0 57 1014
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 208 5.7 %
Rwork0.301 3464 -
obs--66.1 %
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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