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- PDB-7clg: Crystal structure of the ATP-dependent restriction endonuclease SauUSI -

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Basic information

Entry
Database: PDB / ID: 7clg
TitleCrystal structure of the ATP-dependent restriction endonuclease SauUSI
ComponentsPutative helicase
KeywordsDNA BINDING PROTEIN / Restriction endonuclease / ATPase / helicase / SRA
Function / homology
Function and homology information


helicase activity / DNA binding / ATP binding
Similarity search - Function
Protein of unknown function DUF3427 / Domain of unknown function (DUF3427) / Phospholipase D-like domain / PLD-like domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. ...Protein of unknown function DUF3427 / Domain of unknown function (DUF3427) / Phospholipase D-like domain / PLD-like domain / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus subsp. aureus USA300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsSaikrishnan, K. / Tumuluri, V.S.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Mechanism of DNA cleavage by the endonuclease SauUSI: a major barrier to horizontal gene transfer and antibiotic resistance in Staphylococcus aureus.
Authors: Tumuluri, V.S. / Rajgor, V. / Xu, S.Y. / Chouhan, O.P. / Saikrishnan, K.
History
DepositionJul 21, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 4, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative helicase
B: Putative helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,3406
Polymers221,9562
Non-polymers3844
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-97 kcal/mol
Surface area72490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.583, 175.679, 89.379
Angle α, β, γ (deg.)90.000, 115.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative helicase / / ATP-dependent restriction endonuclease / SauUSI


Mass: 110977.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus USA300 (bacteria)
Strain: USA300 / Gene: SAUSA300_2431 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2XK17
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate, 11% to 14% PEG 4000' 0.25 M to 0.4 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97954 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 3.1→87.8 Å / Num. obs: 85717 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.1
Reflection shellResolution: 3.1→3.22 Å / Rmerge(I) obs: 1.2 / Num. unique obs: 4572

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→56.79 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 35.81 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2967 3967 4.63 %
Rwork0.2447 81762 -
obs0.2472 85717 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 305.66 Å2 / Biso mean: 129.5509 Å2 / Biso min: 39.57 Å2
Refinement stepCycle: final / Resolution: 3.1→56.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12275 0 20 33 12328
Biso mean--109.39 95.56 -
Num. residues----1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512501
X-RAY DIFFRACTIONf_angle_d0.75216976
X-RAY DIFFRACTIONf_chiral_restr0.0441979
X-RAY DIFFRACTIONf_plane_restr0.0052181
X-RAY DIFFRACTIONf_dihedral_angle_d15.087390
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1004-3.13830.45211570.3282897100
3.1383-3.1780.35771380.32462928100
3.178-3.21980.34891810.32112923100
3.2198-3.26390.42341460.31632905100
3.2639-3.31050.31111190.2992956100
3.3105-3.35990.39841100.30352939100
3.3599-3.41240.43391570.29332910100
3.4124-3.46840.38421550.3055292799
3.4684-3.52820.30281390.28872879100
3.5282-3.59230.36151420.27882985100
3.5923-3.66140.32861490.2664285199
3.6614-3.73610.32551290.2793299499
3.7361-3.81730.31771060.25752896100
3.8173-3.90610.30651420.2777298199
3.9061-4.00380.34781200.26922845100
4.0038-4.1120.30411320.25773030100
4.112-4.2330.30941180.23362904100
4.233-4.36950.2771650.22342879100
4.3695-4.52560.27791370.21592951100
4.5256-4.70680.20831040.20172979100
4.7068-4.92090.23521460.19722922100
4.9209-5.18010.24561540.21272910100
5.1801-5.50440.26851530.2282899100
5.5044-5.9290.25841100.24842974100
5.929-6.52490.2521600.25952898100
6.5249-7.46730.32411460.26672898100
7.4673-9.4010.31371950.2125286699
9.401-56.790.28141570.2287283698
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)
14.41991.9493-1.41726.8096-2.02674.8742-0.1096-0.1236-0.274-0.42840.0756-0.5474-0.04540.18940.06770.45650.0127-0.10130.4923-0.04790.4838-11.7071-74.676954.0495
22.15722.10580.78021.31480.94852.4060.1887-0.6660.04860.1355-0.12280.5047-0.3875-1.45160.05981.08010.17930.04091.31790.00951.4472-55.4549-88.72151.9189
31.32580.50340.24383.1678-0.44377.2894-0.1-0.0341-0.3559-0.33950.07730.12370.5481-0.0470.05680.69420.03450.11420.50980.03580.8016-33.6295-97.568247.9969
42.13210.62240.88471.72492.08752.568-0.5955-0.7387-0.065-0.012-0.06221.634-0.2976-0.68110.74932.4982-0.6216-0.43230.8032-0.34280.8777-38.8003-93.087111.1196
51.0348-0.65631.0250.5005-0.36497.1279-0.81120.3191.4083-0.22021.01960.9014-1.2353-1.56840.02471.834-0.651-0.38151.33570.42281.1351-40.3392-81.25267.8596
64.9706-0.97441.21170.8523-0.3453.8368-0.22150.59420.1502-1.19180.3842-0.21390.22780.6131-0.37151.9689-0.37470.41540.8584-0.1280.9749-12.0158-79.272819.7306
71.2563-0.1108-1.67351.60640.59573.99430.3165-0.27310.2434-0.0767-0.03480.0384-0.6550.2867-0.25710.5496-0.0956-0.03360.5168-0.04260.5567-21.8317-47.153973.7967
84.0591-0.2648-1.62852.4542-0.71711.99580.5851-0.85120.74710.0128-0.102-0.4987-0.93540.7377-0.30830.9016-0.36230.18050.9484-0.32050.9354-12.6201-33.641680.0356
92.09580.72933.19053.23463.96168.4169-0.2396-0.7277-0.24260.6367-0.1583-0.71271.32741.005-0.09280.8719-0.6514-0.01972.0564-0.17131.421617.3998-43.30781.741
102.7221-0.27630.74765.5013-1.2975.18810.39110.3760.1038-1.0744-0.21-0.9696-0.43070.753-0.23010.8391-0.37680.3031.1607-0.19441.085914.8314-43.861255.2855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 176 )A2 - 176
2X-RAY DIFFRACTION2chain 'A' and (resid 177 through 382 )A177 - 382
3X-RAY DIFFRACTION3chain 'A' and (resid 383 through 655 )A383 - 655
4X-RAY DIFFRACTION4chain 'A' and (resid 656 through 707 )A656 - 707
5X-RAY DIFFRACTION5chain 'A' and (resid 708 through 796 )A708 - 796
6X-RAY DIFFRACTION6chain 'A' and (resid 797 through 953 )A797 - 953
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 486 )B2 - 486
8X-RAY DIFFRACTION8chain 'B' and (resid 487 through 680 )B487 - 680
9X-RAY DIFFRACTION9chain 'B' and (resid 681 through 844 )B681 - 844
10X-RAY DIFFRACTION10chain 'B' and (resid 845 through 953 )B845 - 953

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