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- PDB-2ygk: Crystal structure of the NurA nuclease from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 2ygk
TitleCrystal structure of the NurA nuclease from Sulfolobus solfataricus
ComponentsNURA
KeywordsHYDROLASE / DNA REPAIR / REPLICATION
Function / homology
Function and homology information


nuclease activity / Hydrolases; Acting on ester bonds / DNA repair / metal ion binding
Similarity search - Function
: / NurA domain / NurA domain / NurA
Similarity search - Domain/homology
: / DNA double-strand break repair nuclease NurA
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRzechorzek, N.J. / Blackwood, J.K. / Abrams, A.S. / Maman, J.D. / Robinson, N.P. / Pellegrini, L.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural and Functional Insights Into DNA-End Processing by the Archaeal Hera Helicase-Nura Nuclease Complex.
Authors: Blackwood, J.K. / Rzechorzek, N.J. / Abrams, A.S. / Maman, J.D. / Pellegrini, L. / Robinson, N.P.
History
DepositionApr 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Other
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NURA
B: NURA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4084
Polymers79,2982
Non-polymers1102
Water1,18966
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-53.4 kcal/mol
Surface area30790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.740, 80.280, 67.670
Angle α, β, γ (deg.)90.00, 107.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2 / Auth seq-ID: 1 - 335 / Label seq-ID: 1 - 335

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.2952, 0.9554), (-0.00023, -1), (0.9554, -0.000212, 0.2952)
Vector: 0.02526, 70.45, -0.0022)

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Components

#1: Protein NURA


Mass: 39649.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Plasmid: PET30A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)ROSETTA / References: UniProt: Q97WH1
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.3 Å3/Da / Density % sol: 46.7 % / Description: NONE
Crystal growpH: 4.5
Details: 0.1 M SODIUM CITRATE PH 4.5, 1 M LITHIUM CHLORIDE, 5% W/V PEG 6K, 50 MM MANGANESE CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9794
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→35.94 Å / Num. obs: 24087 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→35.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / SU B: 28.798 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.01 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.27089 1230 5.1 %RANDOM
Rwork0.23176 ---
obs0.23382 22842 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20.49 Å2
2---2 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5166 0 2 66 5234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225258
X-RAY DIFFRACTIONr_bond_other_d0.0030.023738
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9797050
X-RAY DIFFRACTIONr_angle_other_deg0.88739122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.624.333240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.606151064
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8421538
X-RAY DIFFRACTIONr_chiral_restr0.0740.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025670
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021032
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.53160
X-RAY DIFFRACTIONr_mcbond_other0.1351.51312
X-RAY DIFFRACTIONr_mcangle_it1.81825116
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28532098
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0494.51934
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1888tight positional0.040.05
2B1888tight positional0.040.05
1A2572medium positional0.070.5
2B2572medium positional0.070.5
1A1888tight thermal0.280.5
2B1888tight thermal0.280.5
1A2572medium thermal0.332
2B2572medium thermal0.332
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 75 -
Rwork0.381 1662 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3741-0.5699-0.38265.08140.41711.29020.0075-0.1528-0.19430.2674-0.0121-0.1248-0.0090.04510.00470.1604-0.01510.02460.03750.02340.229218.04347.8099.071
21.5801-0.7324-0.28985.09680.31930.85520.0543-0.12530.01210.1949-0.0025-0.2171-0.1590.162-0.05190.2651-0.04070.05070.04990.01510.1133.35622.63619.922
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 335
2X-RAY DIFFRACTION2B1 - 335

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