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- PDB-1xwm: The crystal structure of PhoU (phosphate uptake regulator), Struc... -

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Basic information

Entry
Database: PDB / ID: 1xwm
TitleThe crystal structure of PhoU (phosphate uptake regulator), Structural genomics
Componentsphosphate uptake regulator
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PhoU / Negative phosphate uptake regulator / protein structure initiative / PSI / MCSG / Midwest center for structural genomics
Function / homologyPhosphate transport system protein phou homolog 2; domain 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsZhang, R. / Dementieva, I. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of PhoU (phosphate uptake regulator)
Authors: Zhang, R. / Dementieva, I. / Moy, S. / Joachimiak, A.
History
DepositionNov 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 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: phosphate uptake regulator


Theoretical massNumber of molelcules
Total (without water)23,8041
Polymers23,8041
Non-polymers00
Water905
1
A: phosphate uptake regulator

A: phosphate uptake regulator


Theoretical massNumber of molelcules
Total (without water)47,6082
Polymers47,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)61.172, 61.172, 121.264
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThis protein exists as dimer. The second part of the dimer is generated by crystallographic two fold axis.

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Components

#1: Protein phosphate uptake regulator / PhoU


Mass: 23804.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: RBSTP1653 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.29 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 16% PEG3350, 0.2M ammonium tartrate, 0.1M Bis-Tris buffer, pH 5.9, 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, 0.94656
DetectorType: SBC-2 / Detector: CCD / Date: Nov 19, 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
20.946561
ReflectionResolution: 2.5→50 Å / Num. all: 15341 / Num. obs: 15295 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 22.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 1.87 / Num. unique all: 1524 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→30.59 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 342821.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.334 691 4.9 %RANDOM
Rwork0.243 ---
obs0.243 14024 92 %-
all-15243 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6805 Å2 / ksol: 0.309509 e/Å3
Displacement parametersBiso mean: 49.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.02 Å20 Å20 Å2
2--6.02 Å20 Å2
3----12.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.5→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1621 0 0 5 1626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 87 4.7 %
Rwork0.346 1781 -
obs--72.7 %
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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