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- PDB-3ez9: Partition Protein -

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Basic information

Entry
Database: PDB / ID: 3ez9
TitlePartition Protein
ComponentsParA
KeywordsBIOSYNTHETIC PROTEIN / dna binding / winged-hth / partition
Function / homologyMultidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #30 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / :
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Newport str. SL317 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSchumacher, M.A.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis for ADP-mediated transcriptional regulation by P1 and P7 ParA.
Authors: Dunham, T.D. / Xu, W. / Funnell, B.E. / Schumacher, M.A.
History
DepositionOct 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ParA
B: ParA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0943
Polymers91,0692
Non-polymers241
Water1,35175
1
A: ParA
hetero molecules

A: ParA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1184
Polymers91,0692
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4940 Å2
ΔGint-31 kcal/mol
Surface area33660 Å2
MethodPISA
2
B: ParA

B: ParA


Theoretical massNumber of molelcules
Total (without water)91,0692
Polymers91,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area4310 Å2
ΔGint-29 kcal/mol
Surface area35240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.950, 267.410, 154.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsdimer

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Components

#1: Protein ParA


Mass: 45534.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Newport str. SL317 (bacteria)
Gene: SNSL317_A0932 / References: UniProt: B4ABW6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 3000, ethylene glycol, 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: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 2, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.78→100.5 Å / Num. obs: 33374 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 52.7 Å2 / Rsym value: 0.048 / Net I/σ(I): 10.1

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Processing

SoftwareName: CNS / Version: 1.2 / Classification: refinement
RefinementResolution: 2.8→66.85 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 0.5 / Data cutoff high absF: 2254383 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2015 6.9 %RANDOM
Rwork0.254 ---
obs-29003 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.177 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 184.8 Å2 / Biso mean: 87.502 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--17.63 Å20 Å20 Å2
2--28.03 Å20 Å2
3----10.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.8→66.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 1 75 5670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 342 7.2 %
Rwork0.383 4432 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramadp.top
X-RAY DIFFRACTION4adp.paramglycerol-hepes.top
X-RAY DIFFRACTION5glycerol-hepes.param.txtwater.top

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