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- PDB-4e09: Structure of ParF-AMPPCP, I422 form -

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Basic information

Entry
Database: PDB / ID: 4000000000
TitleStructure of ParF-AMPPCP, I422 form
ComponentsPlasmid partitioning protein ParF
KeywordsUNKNOWN FUNCTION / Deviant Walker box / DNA segregation
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
CobQ/CobB/MinD/ParA nucleotide binding domain / CobQ/CobB/MinD/ParA nucleotide binding domain / : / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chromosome partitioning protein ParA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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 / 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: Plasmid partitioning protein ParF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6633
Polymers22,0611
Non-polymers6012
Water00
1
A: Plasmid partitioning protein ParF
hetero molecules

A: Plasmid partitioning protein ParF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3256
Polymers44,1232
Non-polymers1,2034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area4330 Å2
ΔGint-25 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.600, 87.600, 150.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Plasmid partitioning protein ParF


Mass: 22061.303 Da / Num. of mol.: 1
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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3000, kCl, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→75.65 Å / Num. all: 6770 / Num. obs: 6763 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.7 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→75.6 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 2596360.6 / 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
Rfree0.299 668 10.9 %RANDOM
Rwork0.277 ---
obs0.277 6125 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.7749 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 92.8 Å2
Baniso -1Baniso -2Baniso -3
1--33.56 Å20 Å20 Å2
2---33.56 Å20 Å2
3---67.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 2.99→75.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 36 0 1567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.99→3.18 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.453 103 11.4 %
Rwork0.479 799 -
obs--89.7 %
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 DIFFRACTION5atp.paramatp-top.top

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