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- PDB-6njw: C-terminal region of the Xanthomonas campestris pv. campestris OL... -

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Basic information

Entry
Database: PDB / ID: 6njw
TitleC-terminal region of the Xanthomonas campestris pv. campestris OLD protein phased with platinum
ComponentsXcc_ctr_pt
KeywordsUNKNOWN FUNCTION / Nuclease / Toprim
Function / homologyOvercoming lysogenization defect protein-like, TOPRIM domain / OLD protein-like, TOPRIM domain / AAA domain, group 15 / AAA ATPase domain / P-loop containing nucleoside triphosphate hydrolase / IODIDE ION / : / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsSchiltz, C.J. / Lee, A. / Partlow, E.A. / Hosford, C.J. / Chappie, J.S.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage.
Authors: Schiltz, C.J. / Lee, A. / Partlow, E.A. / Hosford, C.J. / Chappie, J.S.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xcc_ctr_pt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5105
Polymers26,0361
Non-polymers4734
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.426, 65.426, 63.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Xcc_ctr_pt


Mass: 26036.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain B100) (bacteria)
Strain: B100 / Gene: XCCB100_2436 / Production host: Escherichia coli (E. coli) / References: UniProt: B0RTN2
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis Tris Propane pH 7.0-8.0, 11-26% PEG 3350, and 0.15-0.2 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0716 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 1.86→65.43 Å / Num. obs: 44393 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 42.91 Å2 / Net I/σ(I): 19.5
Reflection shellResolution: 1.86→1.9 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→46.26 Å / SU ML: 0.287 / Cross valid method: FREE R-VALUE / σ(F): 1.77 / Phase error: 26.3421
RfactorNum. reflection% reflection
Rfree0.238 2268 5.11 %
Rwork0.2115 --
obs0.2128 44376 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.24 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 4 73 1724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691677
X-RAY DIFFRACTIONf_angle_d0.82292277
X-RAY DIFFRACTIONf_chiral_restr0.0513261
X-RAY DIFFRACTIONf_plane_restr0.0049303
X-RAY DIFFRACTIONf_dihedral_angle_d8.38991011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.90.42111220.36662694X-RAY DIFFRACTION99.89
1.9-1.940.35871660.32782583X-RAY DIFFRACTION99.82
1.94-1.990.3391640.31122599X-RAY DIFFRACTION99.64
1.99-2.050.34361310.32152668X-RAY DIFFRACTION99.96
2.05-2.110.3191310.28752625X-RAY DIFFRACTION99.89
2.11-2.180.25651540.24592617X-RAY DIFFRACTION99.86
2.18-2.250.2521700.24462612X-RAY DIFFRACTION100
2.25-2.340.26411670.21222606X-RAY DIFFRACTION99.93
2.34-2.450.27051460.21422611X-RAY DIFFRACTION100
2.45-2.580.30571280.21762625X-RAY DIFFRACTION99.96
2.58-2.740.23811250.21742674X-RAY DIFFRACTION100
2.74-2.950.26651550.23072610X-RAY DIFFRACTION99.96
2.95-3.250.25071240.22092650X-RAY DIFFRACTION99.89
3.25-3.720.21261380.20692624X-RAY DIFFRACTION99.96
3.72-4.690.18431330.17552656X-RAY DIFFRACTION99.93
4.69-46.280.20761140.18862654X-RAY DIFFRACTION99.89

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