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- PDB-4q25: Crystal structure of PhoU from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4q25
TitleCrystal structure of PhoU from Pseudomonas aeruginosa
ComponentsPhosphate-specific transport system accessory protein PhoU homolog
KeywordsUNKNOWN FUNCTION / Helix bundle / Membrane
Function / homology
Function and homology information


negative regulation of positive chemotaxis / negative regulation of phosphate transmembrane transport / negative regulation of phosphate metabolic process / negative regulation of chemotaxis / phosphate ion transport / intracellular phosphate ion homeostasis / cell chemotaxis / protein homodimerization activity / cytoplasm
Similarity search - Function
Phosphate transport system protein PhoU / PhoU domain / PhoU domain / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate-specific transport system accessory protein PhoU homolog
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsLee, S.J. / Lee, B.-J. / Suh, S.W.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: Crystal structure of PhoU from Pseudomonas aeruginosa, a negative regulator of the Pho regulon.
Authors: Lee, S.J. / Park, Y.S. / Kim, S.J. / Lee, B.J. / Suh, S.W.
History
DepositionApr 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 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

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Assembly

Deposited unit
A: Phosphate-specific transport system accessory protein PhoU homolog
B: Phosphate-specific transport system accessory protein PhoU homolog


Theoretical massNumber of molelcules
Total (without water)57,1932
Polymers57,1932
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-16 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.483, 70.483, 196.203
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phosphate-specific transport system accessory protein PhoU homolog / Pst system accessory protein PhoU homolog


Mass: 28596.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA5365, phoU / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q51547
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M sodium malonate, pH 4.0, 12% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 22783 / % possible obs: 99.9 %
Reflection shellResolution: 2.28→2.32 Å / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.28→49.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.957 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1170 5.1 %RANDOM
Rwork0.20915 ---
obs0.21041 21595 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.515 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2--1.55 Å20 Å2
3----3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.28→49.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 58 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193355
X-RAY DIFFRACTIONr_bond_other_d0.0010.023318
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9664524
X-RAY DIFFRACTIONr_angle_other_deg0.82737572
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9923.898177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98615631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1361542
X-RAY DIFFRACTIONr_chiral_restr0.0870.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 80 -
Rwork0.275 1572 -
obs--98.74 %

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