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- PDB-1t72: Crystal structure of phosphate transport system protein phoU from... -

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Basic information

Entry
Database: PDB / ID: 1t72
TitleCrystal structure of phosphate transport system protein phoU from Aquifex aeolicus
ComponentsPhosphate transport system protein phoU homolog
KeywordsTRANSPORT PROTEIN / helix bundle / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of phosphate transmembrane transport / negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / negative regulation of gene expression / 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 speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsOganesyan, V. / Kim, S.-H. / Oganesyan, N. / Jancarik, J. / Adams, P.D. / Kim, R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus.
Authors: Oganesyan, V. / Oganesyan, N. / Adams, P.D. / Jancarik, J. / Yokota, H.A. / Kim, R. / Kim, S.H.
History
DepositionMay 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: 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: Phosphate transport system protein phoU homolog
B: Phosphate transport system protein phoU homolog
D: Phosphate transport system protein phoU homolog
E: Phosphate transport system protein phoU homolog
F: Phosphate transport system protein phoU homolog
G: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)158,4826
Polymers158,4826
Non-polymers00
Water2,900161
1
A: Phosphate transport system protein phoU homolog
B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)52,8272
Polymers52,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area20040 Å2
MethodPISA
2
D: Phosphate transport system protein phoU homolog
E: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)52,8272
Polymers52,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-17 kcal/mol
Surface area19770 Å2
MethodPISA
3
F: Phosphate transport system protein phoU homolog
G: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)52,8272
Polymers52,8272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-19 kcal/mol
Surface area19490 Å2
MethodPISA
4
A: Phosphate transport system protein phoU homolog

B: Phosphate transport system protein phoU homolog
D: Phosphate transport system protein phoU homolog
E: Phosphate transport system protein phoU homolog
F: Phosphate transport system protein phoU homolog
G: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)158,4826
Polymers158,4826
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_654-y+1,x,z-1/41
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-71 kcal/mol
Surface area56080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.500, 113.500, 155.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Phosphate transport system protein phoU homolog


Mass: 26413.711 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: B834 / Gene: PHOU, AQ_906 / Plasmid: pB4.1105B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: O67053
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.24 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium chloride, lithium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2004 / Details: double crystal Si(111)
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.795→48 Å / Num. obs: 47223 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 68 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16
Reflection shellHighest resolution: 2.795 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.127 / Mean I/σ(I) obs: 21.6 / Num. unique all: 40410 / Rsym value: 0.127 / % possible all: 84.55

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.9→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.29271 2040 -RANDOM
Rwork0.20078 ---
obs0.21637 38370 84.5 %-
all-44131 --
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.075 Å0.056 Å
Luzzati d res low-6 Å
Luzzati sigma a0.068 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10230 0 0 161 10391
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_angle_refined_deg1.381
X-RAY DIFFRACTIONr_chiral_restr0.08
X-RAY DIFFRACTIONr_gen_planes_refined0.004
X-RAY DIFFRACTIONr_nbd_refined0.29
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.29 2040 -
Rwork0.20078 --
obs-38370 84.55 %

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