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- PDB-4e03: Structure of ParF-ADP form 2 -

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Basic information

Entry
Database: PDB / ID: 4000
TitleStructure of ParF-ADP form 2
ComponentsPlasmid partitioning protein ParF
KeywordsUNKNOWN FUNCTION / partition / segregation / multidrug resistance / deviant Walker box / DNA segregation
Function / homology
Function and homology information


CobQ/CobB/MinD/ParA nucleotide binding domain / CobQ/CobB/MinD/ParA nucleotide binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chromosome partitioning protein ParA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSchumacher, M.A. / Ye, Q. / Barge, M.R. / Barilla, D. / Hayes, F.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Mechanism of ATP-induced Polymerization of the Partition Factor ParF: IMPLICATIONS FOR DNA SEGREGATION.
Authors: Schumacher, M.A. / Ye, Q. / Barge, M.T. / Zampini, M. / Barilla, D. / Hayes, F.
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Plasmid partitioning protein ParF
B: Plasmid partitioning protein ParF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0266
Polymers44,1232
Non-polymers9034
Water2,468137
1
A: Plasmid partitioning protein ParF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5133
Polymers22,0611
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plasmid partitioning protein ParF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5133
Polymers22,0611
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-40 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.650, 80.230, 67.000
Angle α, β, γ (deg.)90.00, 112.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasmid partitioning protein ParF


Mass: 22061.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parF, pOLA52_52 / Production host: Escherichia coli (E. coli) / References: UniProt: B0ZE06
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: peg 6000, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.45→80.1 Å / Num. all: 20000 / Num. obs: 18898 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.1 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→61.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1230368.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1850 9.8 %RANDOM
Rwork0.203 ---
obs0.203 18890 95.7 %-
all-2000 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8561 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.45 Å20 Å2-5.1 Å2
2---3.5 Å20 Å2
3----1.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→61.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 56 137 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.972.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.349 292 9.1 %
Rwork0.277 2904 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION5adp.paramadp.top

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