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- PDB-4umk: The complex of Spo0J and parS DNA in chromosomal partition system -

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Basic information

Entry
Database: PDB / ID: 4umk
TitleThe complex of Spo0J and parS DNA in chromosomal partition system
Components
  • (DNA) x 2
  • PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


positive regulation of sporulation resulting in formation of a cellular spore / chromosome segregation / chromosome / DNA binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #2830 / ParB/Spo0J, HTH domain / HTH domain found in ParB protein / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Probable chromosome-partitioning protein ParB
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
BACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.096 Å
AuthorsChen, B.W. / Chu, C.H. / Tung, J.Y. / Hsu, C.E. / Hsiao, C.D. / Sun, Y.J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015
Title: Insights into ParB spreading from the complex structure of Spo0J and parS.
Authors: Chen, B.W. / Lin, M.H. / Chu, C.H. / Hsu, C.E. / Sun, Y.J.
History
DepositionMay 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
B: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
C: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
D: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
W: DNA
X: DNA
Y: DNA
Z: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,58814
Polymers139,0118
Non-polymers5766
Water4,161231
1
A: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
C: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
W: DNA
X: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8908
Polymers69,5064
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-3.1 kcal/mol
Surface area37520 Å2
MethodPQS
2
B: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
D: PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB
Y: DNA
Z: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6986
Polymers69,5064
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11550 Å2
ΔGint-3.7 kcal/mol
Surface area36810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)54.475, 232.731, 78.342
Angle α, β, γ (deg.)90.00, 109.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROBABLE CHROMOSOME-PARTITIONING PROTEIN PARB / SPO0J


Mass: 27382.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: O25758
#2: DNA chain DNA /


Mass: 7483.842 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria)
#3: DNA chain DNA /


Mass: 7256.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) BACILLUS SUBTILIS (bacteria)
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.53 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 8 / Details: PH 8

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. obs: 33332 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 73.03 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 3.096→23.574 Å / SU ML: 0.47 / σ(F): 0 / Phase error: 35.19 / Stereochemistry target values: ML
Details: CHAIN A RESIDUES 1-54, 227-240 CHAIN B RESIDUES 1-44, 228-240 CHAIN C RESIDUES 1-34, 228-240 CHAIN D RESIDUES 1-50, 227-240 ARE MISSING.
RfactorNum. reflection% reflection
Rfree0.2992 1925 6 %
Rwork0.2509 --
obs0.2539 32160 96.39 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.7 Å2
Refinement stepCycle: LAST / Resolution: 3.096→23.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 1968 30 231 7994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0298163
X-RAY DIFFRACTIONf_angle_d1.87611234
X-RAY DIFFRACTIONf_dihedral_angle_d27.1793268
X-RAY DIFFRACTIONf_chiral_restr0.1081313
X-RAY DIFFRACTIONf_plane_restr0.0071094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0961-3.17340.34151200.29181923X-RAY DIFFRACTION86
3.1734-3.2590.36451340.26422013X-RAY DIFFRACTION91
3.259-3.35460.34671260.24842044X-RAY DIFFRACTION91
3.3546-3.46260.34161360.27442111X-RAY DIFFRACTION94
3.4626-3.58590.36111420.26942156X-RAY DIFFRACTION96
3.5859-3.72890.35411370.25542174X-RAY DIFFRACTION98
3.7289-3.89790.31431410.24282237X-RAY DIFFRACTION98
3.8979-4.10240.31921410.23572164X-RAY DIFFRACTION99
4.1024-4.35790.2871380.22392221X-RAY DIFFRACTION99
4.3579-4.6920.25281440.22032230X-RAY DIFFRACTION99
4.692-5.15970.36471400.25472220X-RAY DIFFRACTION99
5.1597-5.89610.28481430.26232243X-RAY DIFFRACTION100
5.8961-7.39030.34071460.29632251X-RAY DIFFRACTION100
7.3903-23.57460.22171370.23822248X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 59.2522 Å / Origin y: 26.798 Å / Origin z: 34.8308 Å
111213212223313233
T0.3086 Å20.0808 Å20.0176 Å2-0.412 Å20.0138 Å2--0.365 Å2
L-0.1593 °20.0725 °2-0.0089 °2-0.0154 °2-0.0182 °2---0.1339 °2
S0.0232 Å °-0.042 Å °0.0384 Å °-0.0124 Å °0.0133 Å °0.0216 Å °0.0138 Å °0.0781 Å °-0.0369 Å °
Refinement TLS groupSelection details: ALL

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