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- PDB-3ez7: Partition Protein Apo form in space group I4122 -

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Basic information

Entry
Database: PDB / ID: 3ez7
TitlePartition Protein Apo form in space group I4122
ComponentsPlasmid partition protein A
KeywordsDNA BINDING PROTEIN / partition / dna binding / winged-hth / Plasmid / Plasmid partition
Function / homology
Function and homology information


plasmid partitioning / identical protein binding
Similarity search - Function
ParA helix turn helix domain / ParA helix turn helix domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #30 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle ...ParA helix turn helix domain / ParA helix turn helix domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #30 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Plasmid partition protein A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.92 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plasmid partition protein A


Theoretical massNumber of molelcules
Total (without water)44,3271
Polymers44,3271
Non-polymers00
Water34219
1
A: Plasmid partition protein A

A: Plasmid partition protein A


Theoretical massNumber of molelcules
Total (without water)88,6552
Polymers88,6552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area11440 Å2
ΔGint-106 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.300, 145.300, 126.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Plasmid partition protein A


Mass: 44327.398 Da / Num. of mol.: 1 / Mutation: K122Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: p1 bacteriophage / Gene: p1, parA / Plasmid: pET15-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07620
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Formate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0, 1.26554, 1.26541, 1.3500
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 2, 2007
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.265541
31.265411
41.351
ReflectionResolution: 2.92→72.6 Å / Num. obs: 15343 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: -0.1 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.92→57.77 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2498555.22 / 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
Rfree0.283 1514 10.2 %RANDOM
Rwork0.24 ---
obs0.24 14899 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.376 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 94.7 Å2
Baniso -1Baniso -2Baniso -3
1-15.01 Å20 Å20 Å2
2--15.01 Å20 Å2
3----30.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.87 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 2.92→57.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 0 19 2999
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.81.5
X-RAY DIFFRACTIONc_mcangle_it4.82
X-RAY DIFFRACTIONc_scbond_it3.52
X-RAY DIFFRACTIONc_scangle_it5.532.5
LS refinement shellResolution: 2.92→3.1 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.452 268 10.9 %
Rwork0.381 2183 -
obs--99.6 %
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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