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- PDB-1mwk: ParM from plasmid R1 APO form -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1mwk
TitleParM from plasmid R1 APO form
ComponentsParM
KeywordsSTRUCTURAL PROTEIN / plasmid / plasmid partition
Function / homology
Function and homology information


plasmid partitioning / identical protein binding
Similarity search - Function
Plasmid segregation protein ParM/StbA / : / Plasmid segregation protein ParM, N-terminal / Plasmid segregation protein ParM, C-terminal / ParM-like / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Plasmid segregation protein ParM
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVan den Ent, F. / Moller-Jensen, J. / Amos, L.A. / Gerdes, K. / Lowe, J.
CitationJournal: EMBO J. / Year: 2002
Title: F-actin-like filaments formed by plasmid segregation protein ParM
Authors: Van den Ent, F. / Moller-Jensen, J. / Amos, L.A. / Gerdes, K. / Lowe, J.
History
DepositionSep 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: ParM
B: ParM


Theoretical massNumber of molelcules
Total (without water)71,6092
Polymers71,6092
Non-polymers00
Water5,080282
1
A: ParM


Theoretical massNumber of molelcules
Total (without water)35,8041
Polymers35,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ParM


Theoretical massNumber of molelcules
Total (without water)35,8041
Polymers35,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.68, 72.46, 87.56
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein ParM / Protein StbA / ParA locus 36 kDa protein


Mass: 35804.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: parM / Plasmid: pMD137 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P11904
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5M Na3-citrate, 90mM Guanidinium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 19 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.4-1.6 M1reservoirpH6.5Na3
280-100 mMguanidine-HCl1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→40.5 Å / Num. all: 31145 / Num. obs: 31145 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection
*PLUS
Redundancy: 3.1 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
TRUNCATEdata reduction
CNSrefinement
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.266 1664 random
Rwork0.217 --
all0.2196 33988 -
obs0.2196 33526 -
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4985 0 0 282 5267
Refinement
*PLUS
Lowest resolution: 500 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.193

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