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- PDB-4rs7: Structure of pNOB8 ParB-C -

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Basic information

Entry
Database: PDB / ID: 4rs7
TitleStructure of pNOB8 ParB-C
ComponentsParB-C
KeywordsDNA BINDING PROTEIN / histone-like fold / DNA segregation
Function / homology: / Ssol_1539-like, second domain / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / identical protein binding / ParB/Sulfiredoxin domain-containing protein
Function and homology information
Biological speciesSulfolobus sp. NOB8H2 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsSchumacher, M.A. / Lee, J. / Chinnam, N.B. / Barilla, D.
CitationJournal: Science / Year: 2015
Title: Structures of archaeal DNA segregation machinery reveal bacterial and eukaryotic linkages.
Authors: Schumacher, M.A. / Tonthat, N.K. / Lee, J. / Rodriguez-Castaneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: ParB-C
D: ParB-C
A: ParB-C
B: ParB-C


Theoretical massNumber of molelcules
Total (without water)46,9004
Polymers46,9004
Non-polymers00
Water6,593366
1
R: ParB-C
D: ParB-C


Theoretical massNumber of molelcules
Total (without water)23,4502
Polymers23,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-50 kcal/mol
Surface area9730 Å2
MethodPISA
2
A: ParB-C
B: ParB-C


Theoretical massNumber of molelcules
Total (without water)23,4502
Polymers23,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-53 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.210, 56.060, 72.300
Angle α, β, γ (deg.)90.00, 94.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ParB-C


Mass: 11725.104 Da / Num. of mol.: 4 / Fragment: UNP residues 375-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus sp. NOB8H2 (acidophilic) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O93707
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, PEG8000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979, 0.980, 0.9252
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 22, 2013
RadiationMonochromator: double flat crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.981
30.92521
ReflectionResolution: 1.9→37.34 Å / Num. all: 59766 / Num. obs: 59754 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→37.34 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 3881 6.49 %RANDOM
Rwork0.1931 ---
obs0.1951 59754 96.38 %-
all-59766 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.72 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7354 Å2-0 Å21.57 Å2
2---7.234 Å2-0 Å2
3---3.4986 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2987 0 0 366 3353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043051
X-RAY DIFFRACTIONf_angle_d0.7114098
X-RAY DIFFRACTIONf_dihedral_angle_d14.891191
X-RAY DIFFRACTIONf_chiral_restr0.051433
X-RAY DIFFRACTIONf_plane_restr0.003513
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.96780.30823720.25155647X-RAY DIFFRACTION97
1.9678-2.04650.27114200.21855617X-RAY DIFFRACTION98
2.0465-2.13970.23973620.20525680X-RAY DIFFRACTION97
2.1397-2.25250.25714260.20845618X-RAY DIFFRACTION97
2.2525-2.39360.21743650.19825589X-RAY DIFFRACTION96
2.3936-2.57830.21923990.19025598X-RAY DIFFRACTION97
2.5783-2.83770.28093750.20385565X-RAY DIFFRACTION96
2.8377-3.24810.23443770.19925521X-RAY DIFFRACTION95
3.2481-4.09150.18423920.16975563X-RAY DIFFRACTION96
4.0915-37.34750.19593930.17695475X-RAY DIFFRACTION95

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