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- PDB-2jd3: ParR from plasmid pB171 -

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Basic information

Entry
Database: PDB / ID: 2jd3
TitleParR from plasmid pB171
ComponentsSTBB PROTEIN
KeywordsDNA BINDING PROTEIN / PLASMID SEGREGATION / ACTIN-LIKE FILAMENTS / RHH2 / PARM / PLASMID / DNA BINDING
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #20 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix non-globular / Special / :
Function and homology information
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsMoller-Jensen, J. / Lowe, J.
CitationJournal: Embo J. / Year: 2007
Title: Structural Analysis of the Parr/Parc Plasmid Partition Complex.
Authors: Moller-Jensen, J. / Ringgaard, S. / Mercogliano, C.P. / Gerdes, K. / Lowe, J.
History
DepositionJan 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STBB PROTEIN
B: STBB PROTEIN


Theoretical massNumber of molelcules
Total (without water)29,3382
Polymers29,3382
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-63.3 kcal/mol
Surface area12210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.768, 96.768, 124.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein STBB PROTEIN / PARR / STABILITY PROTEIN


Mass: 14668.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Description: PLASMID PB171 (ORF 67) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9S101
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.91 Å3/Da / Density % sol: 58 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 9015 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 80.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 12 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.8→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2767 469 5.2 %RANDOM
Rwork0.2394 ---
obs0.2394 8997 99.8 %-
Solvent computationBsol: 31.7018 Å2 / ksol: 0.321467 e/Å3
Displacement parametersBiso mean: 54.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.332 Å2-10.149 Å20 Å2
2---0.332 Å20 Å2
3---0.664 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 0 26 1460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.347
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 9
Rfactor% reflection
Rfree0.4538 5 %
Rwork0.3787 -
obs-99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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