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- PDB-6nk8: C-terminal region of the Burkholderia pseudomallei OLD protein -

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Basic information

Entry
Database: PDB / ID: 6nk8
TitleC-terminal region of the Burkholderia pseudomallei OLD protein
ComponentsClass 2 OLD family nuclease
KeywordsUNKNOWN FUNCTION / Nuclease / Toprim
Function / homologyOLD protein-like, TOPRIM domain / AAA domain, group 15 / AAA ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Uncharacterized protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 5, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Class 2 OLD family nuclease
B: Class 2 OLD family nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7618
Polymers51,6162
Non-polymers1466
Water1,40578
1
A: Class 2 OLD family nuclease
B: Class 2 OLD family nuclease
hetero molecules

A: Class 2 OLD family nuclease
B: Class 2 OLD family nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,52316
Polymers103,2314
Non-polymers29212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area6030 Å2
ΔGint-77 kcal/mol
Surface area36250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.256, 105.669, 123.764
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-804-

HOH

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Components

#1: Protein Class 2 OLD family nuclease


Mass: 25807.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain 668) (bacteria)
Strain: 668 / Gene: BURPS668_A0038 / Production host: Escherichia coli (E. coli) / References: UniProt: A3NFC3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.64 Å3/Da / Density % sol: 53.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 0.23 M MgCl2, 30% PEG 400 and 0.001 M glutathione

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.24→65.3 Å / Num. obs: 26567 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.38 Å2 / Net I/σ(I): 18.2
Reflection shellResolution: 2.24→2.31 Å

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→61.88 Å / SU ML: 0.2475 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.2838
RfactorNum. reflection% reflection
Rfree0.2605 1278 4.81 %
Rwork0.2136 --
obs0.2159 26561 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.35 Å2
Refinement stepCycle: LAST / Resolution: 2.24→61.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3128 0 6 78 3212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773191
X-RAY DIFFRACTIONf_angle_d0.90794347
X-RAY DIFFRACTIONf_chiral_restr0.049499
X-RAY DIFFRACTIONf_plane_restr0.006574
X-RAY DIFFRACTIONf_dihedral_angle_d7.91551909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.330.3181460.26942712X-RAY DIFFRACTION97.71
2.33-2.430.25111340.23342780X-RAY DIFFRACTION99.83
2.43-2.560.31591400.21952800X-RAY DIFFRACTION99.76
2.56-2.720.23291460.20862784X-RAY DIFFRACTION99.83
2.72-2.930.26351430.20732809X-RAY DIFFRACTION99.8
2.93-3.230.27781310.21042818X-RAY DIFFRACTION99.83
3.23-3.690.23551370.20452822X-RAY DIFFRACTION99.63
3.69-4.650.22971520.19262840X-RAY DIFFRACTION99.5
4.65-61.910.27881490.22152918X-RAY DIFFRACTION98.33

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