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- PDB-6p74: OLD nuclease from Thermus Scotoductus -

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Basic information

Entry
Database: PDB / ID: 6p74
TitleOLD nuclease from Thermus Scotoductus
ComponentsPutative ATP-dependent endonuclease of the OLD family
KeywordsHYDROLASE / ABC ATPase / Nuclease
Function / homologyOLD protein-like, TOPRIM domain / AAA domain, group 15 / AAA ATPase domain / endonuclease activity / P-loop containing nucleoside triphosphate hydrolase / : / SAMARIUM (III) ION / Putative ATP-dependent endonuclease of the OLD family
Function and homology information
Biological speciesThermus scotoductus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChappie, J.S. / Schiltz, C.J.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: The full-length structure of Thermus scotoductus OLD defines the ATP hydrolysis properties and catalytic mechanism of Class 1 OLD family nucleases.
Authors: Schiltz, C.J. / Adams, M.C. / Chappie, J.S.
History
DepositionJun 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: 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_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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ATP-dependent endonuclease of the OLD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,84915
Polymers59,8251
Non-polymers2,02414
Water1,18966
1
A: Putative ATP-dependent endonuclease of the OLD family
hetero molecules

A: Putative ATP-dependent endonuclease of the OLD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,69830
Polymers119,6502
Non-polymers4,04828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_566x,-y+1,-z+3/21
Buried area12270 Å2
ΔGint-347 kcal/mol
Surface area48070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.362, 101.737, 202.753
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative ATP-dependent endonuclease of the OLD family


Mass: 59825.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus scotoductus (bacteria) / Gene: TSC_c04750 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E8PLM2

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Non-polymers , 5 types, 80 molecules

#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sm
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.59 Å3/Da / Density % sol: 65.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaOAc pH 5.8, 0.3 M AmSO4, 7% PEG MME 2000, and 5 mM SmCl3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0718 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.12→101.38 Å / Num. obs: 49235 / % possible obs: 100 % / Redundancy: 18.1 % / Net I/σ(I): 17.6
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 741

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→101.377 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.64 / Phase error: 27.5
RfactorNum. reflection% reflection
Rfree0.2291 4000 4.79 %
Rwork0.1926 --
obs0.1943 44131 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 335.82 Å2 / Biso mean: 91.7966 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.2→101.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4076 0 139 66 4281
Biso mean--201.51 74.78 -
Num. residues----512
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.22590.43841200.43292360248087
2.2259-2.25310.39821150.4222573268891
2.2531-2.28160.43681380.42712478261690
2.2816-2.31160.34471440.31122787293199
2.3116-2.34330.34851570.30212696285399
2.3433-2.37680.30011250.293628252950100
2.3768-2.41230.33751420.283627912933100
2.4123-2.450.27891360.281327372873100
2.45-2.49010.30281550.271227302885100
2.4901-2.53310.26521020.272728462948100
2.5331-2.57910.29171490.266127662915100
2.5791-2.62870.33871810.274827212902100
2.6287-2.68240.3171540.281128272981100
2.6824-2.74070.33451410.273327172858100
2.7407-2.80450.28411670.246627602927100
2.8045-2.87460.30341590.234327572916100
2.8746-2.95240.26741000.240528052905100
2.9524-3.03920.31871270.249827502877100
3.0392-3.13740.32791380.243827832921100
3.1374-3.24950.3371360.239128002936100
3.2495-3.37960.26271410.240327962937100
3.3796-3.53340.30091220.215427652887100
3.5334-3.71970.26141360.192327502886100
3.7197-3.95280.24761360.175828252961100
3.9528-4.2580.18811500.163727562906100
4.258-4.68650.17311290.148828042933100
4.6865-5.36460.15511610.148127402901100
5.3646-6.75860.19731180.175428222940100
6.7586-101.48420.1521210.136827852906100
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)
13.17640.95891.70585.86123.12846.3590.0128-0.3691-0.16781.38440.0301-0.05520.46790.1967-0.07070.90420.16480.08640.49660.03230.561857.79557.528141.558
24.26560.03920.84735.9313-0.67417.0729-0.2657-0.24550.74070.7161-0.11370.1237-0.60590.0310.41040.94910.16490.14380.5755-0.08920.876152.46369.736137.751
34.122-2.03980.34243.30462.43923.2077-0.4509-1.27530.882-0.66430.1504-0.25170.95190.70140.2811.58590.04780.28081.31710.13151.336635.73845.624146.253
40.51990.52831.31632.79492.88655.83310.0512-0.1120.1171-0.2737-0.4790.5153-0.2791-0.89290.48670.63880.13810.03720.7996-0.15440.998223.66958.659154.996
56.64810.99191.86851.34283.3058.1797-0.15130.15060.4909-0.3721-0.67930.713-0.6636-0.14240.88510.60650.0006-0.00010.767-0.00950.855827.05557.43153.365
62222222.586-9.9143-6.91038.9734-2.6202-4.235322.46837.6903-0.00811.84710.1519-0.37511.49710.19540.788240.4134.287151.408
74.70231.0929-2.60746.4595-1.8083.95780.12770.4221-0.1548-0.2431-0.18160.3048-0.0334-0.26840.11340.57440.1028-0.02550.6324-0.10880.601942.9343.074132.434
83.3665-1.2278-1.16793.94520.47451.9462-0.0737-0.03430.18110.27450.0797-0.1408-0.0635-0.0094-0.03020.50970.08420.02680.47490.02240.362664.88635.53123.776
93.9684.71743.52886.77015.55344.9028-0.27270.6513-0.02020.06760.2937-0.06720.41960.9004-0.070.66170.13350.00970.6303-0.00110.594370.91526.716100.821
107.39790.97620.70972.7415-0.39984.11570.0109-0.5496-0.89530.4302-0.02480.26950.5813-0.38090.02940.61730.11460.06850.47090.09380.587673.65518.371121.211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:67 )A1 - 67
2X-RAY DIFFRACTION2( CHAIN A AND RESID 68:141 )A68 - 141
3X-RAY DIFFRACTION3( CHAIN A AND RESID 142:153 )A142 - 153
4X-RAY DIFFRACTION4( CHAIN A AND RESID 154:208 )A154 - 208
5X-RAY DIFFRACTION5( CHAIN A AND RESID 209:237 )A209 - 237
6X-RAY DIFFRACTION6( CHAIN A AND RESID 245:245 )A245
7X-RAY DIFFRACTION7( CHAIN A AND RESID 246:318 )A246 - 318
8X-RAY DIFFRACTION8( CHAIN A AND RESID 319:435 )A319 - 435
9X-RAY DIFFRACTION9( CHAIN A AND RESID 436:470 )A436 - 470
10X-RAY DIFFRACTION10( CHAIN A AND RESID 471:525 )A471 - 525

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