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- PDB-5k5d: Structure of the C2221 form of Pnob8-like ParB-N domain -

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Basic information

Entry
Database: PDB / ID: 5k5d
TitleStructure of the C2221 form of Pnob8-like ParB-N domain
ComponentsParB domain protein nuclease
KeywordsHYDROLASE / ParB-N / pnob8 / partition
Function / homology: / Ssol_1539-like, second domain / ParB N-terminal domain / ParB/Sulfiredoxin / ParB-like nuclease domain / ParB/Sulfiredoxin superfamily / CITRIC ACID / ParB domain protein nuclease
Function and homology information
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSchumacher, M.
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-Castneda, F.A. / Chinnam, N.B. / Kalliomaa-Sanford, A.K. / Ng, I.W. / Barge, M.T. / Shaw, P.L. / Barilla, D.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: ParB domain protein nuclease
A: ParB domain protein nuclease
C: ParB domain protein nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,2957
Polymers106,5263
Non-polymers7684
Water1,856103
1
A: ParB domain protein nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7012
Polymers35,5091
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ParB domain protein nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7012
Polymers35,5091
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ParB domain protein nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8933
Polymers35,5091
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.030, 98.700, 307.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ParB domain protein nuclease


Mass: 35508.680 Da / Num. of mol.: 3 / Fragment: UNP residues 1-298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: 98/2 / Gene: Ssol_1539 / Production host: Escherichia coli (E. coli) / References: UniProt: D0KSP7
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsprotein had degraded within its C-terminal domain during crystallization

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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: 2.53 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→46.107 Å / Num. obs: 38446 / % possible obs: 95.57 % / Redundancy: 4.3 % / Rsym value: 0.08 / Net I/σ(I): 10.9
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.39 / % possible all: 83.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5K5A

5k5a


Resolution: 2.45→46.107 Å / FOM work R set: 0.8177 / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2623 2000 5.2 %
Rwork0.2222 36446 -
obs0.2243 38446 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.835 Å2 / ksol: 0.396 e/Å3
Displacement parametersBiso max: 265.11 Å2 / Biso mean: 60.69 Å2 / Biso min: 18.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.4702 Å2-0 Å20 Å2
2---6.5123 Å2-0 Å2
3---4.042 Å2
Refinement stepCycle: final / Resolution: 2.45→46.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6255 0 52 103 6410
Biso mean--84.38 51.98 -
Num. residues----751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036379
X-RAY DIFFRACTIONf_angle_d0.6298554
X-RAY DIFFRACTIONf_chiral_restr0.043957
X-RAY DIFFRACTIONf_plane_restr0.0021092
X-RAY DIFFRACTIONf_dihedral_angle_d16.0422561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4499-2.53750.41591670.34973032319980
2.5375-2.63910.34881920.32563505369794
2.6391-2.75920.34392040.29143731393599
2.7592-2.90460.32372050.26713729393499
2.9046-3.08660.30842050.2383748395399
3.0866-3.32480.2712050.23433723392899
3.3248-3.65930.28182040.22583719392398
3.6593-4.18850.22652060.19953750395698
4.1885-5.27580.22012040.18183729393397
5.2758-46.11510.23852080.20873780398894

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