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- PDB-4a62: ParM from R1 plasmid in complex with peptide from C-terminus of ParR -

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Basic information

Entry
Database: PDB / ID: 4a62
TitleParM from R1 plasmid in complex with peptide from C-terminus of ParR
Components
  • PLASMID SEGREGATION PROTEIN PARM
  • PROTEIN STBB
KeywordsTRANSPORT PROTEIN / PLASMID SEGREGATION
Function / homology
Function and homology information


plasmid partitioning / identical protein binding
Similarity search - Function
Plasmid stability protein, StbB / StbB superfamily / Plasmid stability protein / 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 ...Plasmid stability protein, StbB / StbB superfamily / Plasmid stability protein / 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 / Protein StbB
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGayathri, 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 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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

Downloads & links

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Assembly

Deposited unit
A: PLASMID SEGREGATION PROTEIN PARM
B: PLASMID SEGREGATION PROTEIN PARM
C: PROTEIN STBB
D: PROTEIN STBB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6068
Polymers75,5454
Non-polymers1,0614
Water6,936385
1
A: PLASMID SEGREGATION PROTEIN PARM
C: PROTEIN STBB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3034
Polymers37,7732
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-22 kcal/mol
Surface area14930 Å2
MethodPISA
2
B: PLASMID SEGREGATION PROTEIN PARM
D: PROTEIN STBB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3034
Polymers37,7732
Non-polymers5312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-20.7 kcal/mol
Surface area14710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.850, 146.850, 171.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2075-

HOH

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Components

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


Mass: 35762.297 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: PLASMID PROTEIN FROM R1 PLASMID / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI BL21 (bacteria) / Variant (production host): AI / References: UniProt: P11904
#2: Protein/peptide PROTEIN STBB / PARR FROM PLASMID R1


Mass: 2010.269 Da / Num. of mol.: 2 / Fragment: C-TERMINAL HELIX, RESIDUES 101-117 / Source method: obtained synthetically / Details: PLASMID PROTEIN FROM R1 PLASMID / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P11906
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 385 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 163 TO ALA ENGINEERED RESIDUE IN CHAIN B, LEU 163 TO ALA
Nonpolymer detailsMAGNESIUM ION (MG): MG 2+ ION

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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: 2.21 Å3/Da / Density % sol: 44.32 % / Description: NONE
Crystal growpH: 7 / Details: 0.1 M CITRIC ACID PH 5.0, 2.4 M AMMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→34.04 Å / Num. obs: 36167 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 34.34 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 20
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

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

1mwm


Resolution: 2.2→32.615 Å / SU ML: 0.69 / σ(F): 0 / Phase error: 27.55 / Stereochemistry target values: ML
Details: HYDROGENS ADDED IN RIDING POSITIONS DURING REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2688 1810 5 %
Rwork0.2009 --
obs0.2043 36164 99.99 %
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.107 Å2 / ksol: 0.443 e/Å3
Displacement parametersBiso mean: 31.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.2546 Å20 Å20 Å2
2--2.2546 Å20 Å2
3----4.5092 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 64 385 5657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065358
X-RAY DIFFRACTIONf_angle_d1.0167273
X-RAY DIFFRACTIONf_dihedral_angle_d13.891981
X-RAY DIFFRACTIONf_chiral_restr0.055841
X-RAY DIFFRACTIONf_plane_restr0.003929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25950.35641410.26252630X-RAY DIFFRACTION100
2.2595-2.32590.36231300.25152635X-RAY DIFFRACTION100
2.3259-2.4010.31891410.23732596X-RAY DIFFRACTION100
2.401-2.48680.28441270.22212647X-RAY DIFFRACTION100
2.4868-2.58630.31241280.21672598X-RAY DIFFRACTION100
2.5863-2.7040.29751450.23342631X-RAY DIFFRACTION100
2.704-2.84650.28081400.21432631X-RAY DIFFRACTION100
2.8465-3.02470.33081280.23122634X-RAY DIFFRACTION100
3.0247-3.2580.30481580.22992628X-RAY DIFFRACTION100
3.258-3.58550.28141500.20662629X-RAY DIFFRACTION100
3.5855-4.10350.2431330.17482672X-RAY DIFFRACTION100
4.1035-5.16660.19951460.15432661X-RAY DIFFRACTION100
5.1666-32.6190.22221430.17932762X-RAY DIFFRACTION100

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