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- PDB-1tp6: 1.5 A Crystal Structure of a NTF-2 Like Protein of Unknown Functi... -

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Basic information

Entry
Database: PDB / ID: 1tp6
Title1.5 A Crystal Structure of a NTF-2 Like Protein of Unknown Function PA1314 from Pseudomonas aeruginosa
Componentshypothetical protein PA1314
Keywordsstructural genomics / unknown function / Pseudomonas aeruginosa / alpha-beta sandwich / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised conserved protein UCP029394 / Domain of unknown function DUF4440 / Domain of unknown function (DUF4440) / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF4440 domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsZhang, R. / Xu, L.X. / 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 PA1314 from Pseudomonas aeruginosa
Authors: Zhang, R. / Xu, L.X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJun 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PA1314


Theoretical massNumber of molelcules
Total (without water)14,2341
Polymers14,2341
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.802, 36.309, 29.570
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number5
Space group name H-MC121
DetailsThis protein existed as monomer. The deposited coords. represents the monomer in the asymmtric unit.

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Components

#1: Protein hypothetical protein PA1314


Mass: 14234.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Species: Pseudomonas aeruginosa / Strain: PA01 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9I430
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 1.741 Å3/Da / Density % sol: 27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1 M Sodium Acetate, 0.2 M Sodium Citrate, 4% Glycerol, 25% PEG 3350, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795,0.9797,0.94656
DetectorType: SBC-3 / Detector: CCD / Date: May 29, 2004 / 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: 1.5→50 Å / Num. all: 31652 / Num. obs: 30861 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 4.4 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 35.07
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.8 / Num. unique all: 3202 / % possible all: 80.7

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.06 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1485 -RANDOM
Rwork0.185 ---
all0.195 31731 --
obs0.195 30081 94.8 %-
Displacement parametersBiso mean: 16.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-2.22 Å2
2---2.6 Å20 Å2
3---1.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 0 143 1127
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.258 189 -
Rwork0.231 --
obs-3901 77.5 %

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