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- PDB-3kz5: Structure of cdomain -

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Basic information

Entry
Database: PDB / ID: 3kz5
TitleStructure of cdomain
ComponentsProtein sopB
KeywordsDNA BINDING PROTEIN / partition / segregation / F plasmid / DNA-binding protein / DNA-binding
Function / homology
Function and homology information


plasmid partitioning / DNA binding
Similarity search - Function
Helix Hairpins - #1550 / SopB, HTH domain / Centromere-binding protein HTH domain / ParB/RepB/Spo0J partition protein / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
ACETATE ION / Protein SopB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.58 Å
AuthorsSchumacher, M.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Insight into F plasmid DNA segregation revealed by structures of SopB and SopB-DNA complexes.
Authors: Schumacher, M.A. / Piro, K.M. / Xu, W.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Feb 21, 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
E: Protein sopB
B: Protein sopB
A: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4674
Polymers17,4083
Non-polymers591
Water3,081171
1
E: Protein sopB
B: Protein sopB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6653
Polymers11,6052
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-23 kcal/mol
Surface area5990 Å2
MethodPISA
2
A: Protein sopB

A: Protein sopB


Theoretical massNumber of molelcules
Total (without water)11,6052
Polymers11,6052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2640 Å2
ΔGint-22 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.010, 45.400, 36.330
Angle α, β, γ (deg.)90.00, 100.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein sopB / Plasmid partition protein B


Mass: 5802.745 Da / Num. of mol.: 3 / Fragment: UNP residues 276-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12
Description: sopB(272-323) artificial gene for expression in pET15b
Gene: B, ECOK12F047, sopB / Plasmid: pet15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62558
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 4000, sodium acetate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 7, 2009 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.58→43.85 Å / Num. all: 19742 / Num. obs: 18124 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.58→43.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 991750.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1759 9.8 %RANDOM
Rwork0.198 ---
obs0.198 17947 91.2 %-
all-18124 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.0656 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-2.88 Å2
2--2.58 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.58→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1117 0 4 171 1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it2.511.5
X-RAY DIFFRACTIONc_mcangle_it3.482
X-RAY DIFFRACTIONc_scbond_it4.712
X-RAY DIFFRACTIONc_scangle_it6.512.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.425 272 10.3 %
Rwork0.388 2369 -
obs--81.4 %
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 DIFFRACTION5acetate.param.txtacetate.top

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