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- PDB-4a61: ParM from plasmid R1 in complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4a61
TitleParM from plasmid R1 in complex with AMPPNP
ComponentsPLASMID SEGREGATION PROTEIN PARM
KeywordsTRANSPORT PROTEIN / PLASMID SEGREGATION / ACTIN-FOLD
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Plasmid segregation protein ParM
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsvan den Ent, F. / Moller-Jensen, J. / Gayathri, P. / Lowe, J.
CitationJournal: Science / Year: 2012
Title: A bipolar spindle of antiparallel ParM filaments drives bacterial plasmid segregation.
Authors: P Gayathri / T Fujii / J Møller-Jensen / F van den Ent / K Namba / J Löwe /
Abstract: To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between ...To ensure their stable inheritance by daughter cells during cell division, bacterial low-copy-number plasmids make simple DNA segregating machines that use an elongating protein filament between sister plasmids. In the ParMRC system of the Escherichia coli R1 plasmid, ParM, an actinlike protein, forms the spindle between ParRC complexes on sister plasmids. By using a combination of structural work and total internal reflection fluorescence microscopy, we show that ParRC bound and could accelerate growth at only one end of polar ParM filaments, mechanistically resembling eukaryotic formins. The architecture of ParM filaments enabled two ParRC-bound filaments to associate in an antiparallel orientation, forming a bipolar spindle. The spindle elongated as a bundle of at least two antiparallel filaments, thereby pushing two plasmid clusters toward the poles.
History
DepositionOct 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: PLASMID SEGREGATION PROTEIN PARM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2083
Polymers36,6771
Non-polymers5312
Water2,486138
1
A: PLASMID SEGREGATION PROTEIN PARM
hetero molecules

A: PLASMID SEGREGATION PROTEIN PARM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4166
Polymers73,3552
Non-polymers1,0614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4590 Å2
ΔGint-26.9 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.541, 63.541, 164.093
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PLASMID SEGREGATION PROTEIN PARM / PARM FROM PLASMID R1 / PARA LOCUS 36 KDA PROTEIN / PROTEIN STB


Mass: 36677.281 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-320 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: PLASMID R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-AI / References: UniProt: P11904
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 163 TO ARG
Nonpolymer detailsMAGNESIUM ION (MG): MG 2+ ION
Sequence details6X HIS TAG ADDED AT THE N-TERMINUS

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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: 2.3 Å3/Da / Density % sol: 46.56 % / Description: NONE
Crystal growpH: 8.6 / Details: 20% PEG 6000, 100 MM BICINE PH 8.6, 1M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→50.24 Å / Num. obs: 23264 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.3 / % possible all: 90.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_874)refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MWM

1mwm


Resolution: 2→43.335 Å / SU ML: 0.52 / σ(F): 1.37 / Phase error: 22.83 / Stereochemistry target values: ML
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS DURING REFINEMENT. RESIDUES 211-217 AND 241-245 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2528 1109 4.8 %
Rwork0.2094 --
obs0.2114 23202 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.375 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.1519 Å20 Å20 Å2
2--1.1519 Å20 Å2
3----2.3037 Å2
Refinement stepCycle: LAST / Resolution: 2→43.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 32 138 2610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052514
X-RAY DIFFRACTIONf_angle_d0.9363412
X-RAY DIFFRACTIONf_dihedral_angle_d14.301929
X-RAY DIFFRACTIONf_chiral_restr0.051391
X-RAY DIFFRACTIONf_plane_restr0.003434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.09110.33551400.27322434X-RAY DIFFRACTION90
2.0911-2.20130.33161230.23862671X-RAY DIFFRACTION97
2.2013-2.33920.28841300.23722769X-RAY DIFFRACTION100
2.3392-2.51980.26911540.21612741X-RAY DIFFRACTION100
2.5198-2.77340.31821300.21622792X-RAY DIFFRACTION100
2.7734-3.17460.2771530.22192795X-RAY DIFFRACTION100
3.1746-3.99920.24831450.2052853X-RAY DIFFRACTION100
3.9992-43.34530.19281340.18743038X-RAY DIFFRACTION100

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