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- PDB-1vz0: Chromosome segregation protein Spo0J from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 1vz0
TitleChromosome segregation protein Spo0J from Thermus thermophilus
ComponentsChromosome-partitioning protein Spo0J
KeywordsNUCLEAR PROTEIN / CHROMOSOME SEGREGATION / DNA-BINDING / HELIX-TURN-HELIX
Function / homology
Function and homology information


chromosome segregation / DNA binding
Similarity search - Function
Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain - #30 / Arc Repressor Mutant, subunit A - #2830 / ParB/Spo0J, HTH domain / HTH domain found in ParB protein / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily ...Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain - #30 / Arc Repressor Mutant, subunit A - #2830 / ParB/Spo0J, HTH domain / HTH domain found in ParB protein / Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain / ParB/RepB/Spo0J partition protein / ParB/Sulfiredoxin domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / Arc Repressor Mutant, subunit A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / Chromosome-partitioning protein Spo0J
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsLeonard, T.A. / Butler, P.J.G. / Lowe, J.
CitationJournal: Mol. Microbiol. / Year: 2004
Title: Structural analysis of the chromosome segregation protein Spo0J from Thermus thermophilus.
Authors: Leonard, T.A. / Butler, P.J. / Lowe, J.
History
DepositionMay 12, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 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 1.5Jun 20, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type
Revision 1.6May 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

Downloads & links

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Assembly

Deposited unit
A: Chromosome-partitioning protein Spo0J
B: Chromosome-partitioning protein Spo0J
C: Chromosome-partitioning protein Spo0J
D: Chromosome-partitioning protein Spo0J
E: Chromosome-partitioning protein Spo0J
F: Chromosome-partitioning protein Spo0J
G: Chromosome-partitioning protein Spo0J
H: Chromosome-partitioning protein Spo0J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,22723
Polymers204,4128
Non-polymers81515
Water17,745985
1
A: Chromosome-partitioning protein Spo0J
C: Chromosome-partitioning protein Spo0J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4228
Polymers51,1032
Non-polymers3196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Chromosome-partitioning protein Spo0J
G: Chromosome-partitioning protein Spo0J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2805
Polymers51,1032
Non-polymers1773
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
D: Chromosome-partitioning protein Spo0J
H: Chromosome-partitioning protein Spo0J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3046
Polymers51,1032
Non-polymers2014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
E: Chromosome-partitioning protein Spo0J
F: Chromosome-partitioning protein Spo0J
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2214
Polymers51,1032
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)182.240, 295.150, 73.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: Protein
Chromosome-partitioning protein Spo0J


Mass: 25551.475 Da / Num. of mol.: 8 / Fragment: DNA-BINDING DOMAIN, RESIDUES 1-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: spo0C, parB, TT_C1604 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q72H91
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393, 0.9791, 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.93931
20.97911
30.97931
ReflectionResolution: 2.3→50 Å / Num. obs: 87653 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.1
Reflection shellResolution: 2.29→2.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3 / % possible all: 90.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→38.72 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3493551.98 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 4408 5 %RANDOM
Rwork0.235 ---
obs0.235 87419 98.9 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 49.91 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20 Å2
2--5.59 Å20 Å2
3----3.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11878 0 15 985 12878
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
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
Refine LS restraints NCSRms dev Biso : 12.3 Å2 / Rms dev position: 0.16 Å / Weight Biso : 5 / Weight position: 30
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 693 5 %
Rwork0.257 13180 -
obs--95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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