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- PDB-7drs: Structure of SspE_40224 -

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Basic information

Entry
Database: PDB / ID: 7drs
TitleStructure of SspE_40224
ComponentsSspE protein
KeywordsHYDROLASE / DNase / DNA binding protein / GTPase / UNKNOWN FUNCTION
Function / homologyDomain of unknown function DUF1524 / GmrSD restriction endonucleases, C-terminal domain / Domain of unknown function DUF262 / GmrSD restriction endonuclease, N-terminal domain / SspE protein
Function and homology information
Biological speciesStreptomyces yokosukanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsHaiyan, G. / Jinchuan, Z. / Chen, S. / Wang, L. / Wu, G.
CitationJournal: Nat Commun / Year: 2022
Title: Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE.
Authors: Gao, H. / Gong, X. / Zhou, J. / Zhang, Y. / Duan, J. / Wei, Y. / Chen, L. / Deng, Z. / Wang, J. / Chen, S. / Wu, G. / Wang, L.
History
DepositionDec 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: SspE protein
A: SspE protein
B: SspE protein
C: SspE protein


Theoretical massNumber of molelcules
Total (without water)348,5894
Polymers348,5894
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-33 kcal/mol
Surface area124560 Å2
Unit cell
Length a, b, c (Å)111.082, 138.150, 293.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 771 / Label seq-ID: 1 - 771

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAB
2chain BBC
3chain CCD
4chain DDA

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Components

#1: Protein
SspE protein


Mass: 87147.352 Da / Num. of mol.: 4 / Fragment: DUF262 and DUF1524 domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces yokosukanensis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6I8WFL9

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG MME 5000,5% Tascimate,pH 7.0,0.1M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 122839 / % possible obs: 91.4 % / Redundancy: 13.3 % / Rpim(I) all: 0.074 / Net I/σ(I): 1.9
Reflection shellResolution: 3.3→3.42 Å / Num. unique obs: 6612 / CC1/2: 0.779

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.5refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JIV

6jiv


Resolution: 3.42→46.14 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 30.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 5792 4.92 %
Rwork0.2117 --
obs0.2144 117696 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 415 Å2 / Biso mean: 156.4072 Å2 / Biso min: 40.62 Å2
Refinement stepCycle: final / Resolution: 3.42→46.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24548 0 0 0 24548
Num. residues----3084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14515X-RAY DIFFRACTION8.682TORSIONAL
12B14515X-RAY DIFFRACTION8.682TORSIONAL
13C14515X-RAY DIFFRACTION8.682TORSIONAL
14D14515X-RAY DIFFRACTION8.682TORSIONAL
LS refinement shellResolution: 3.42→3.46 Å
RfactorNum. reflection% reflection
Rfree0.4003 --
Rwork0.3574 --
obs-3608 96 %
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)
12.61050.1977-0.05091.7864-0.25681.27210.0088-0.56660.01420.2949-0.02660.03620.05360.0599-0.00010.5874-0.02610.00380.72390.06960.508745.528219.217317.4768
20.11130.38770.13430.3421-0.35412.23160.2282-0.1233-0.1320.1771-0.42690.02360.07820.3393-0.0060.9863-0.1892-0.04491.04660.26530.667948.9203-9.5159349.9269
30.72910.32070.28271.0212-0.24612.4481-0.0186-0.33810.05690.16030.00010.1190.5613-0.2412-0.01180.9898-0.17230.08740.64310.07150.786327.1008-20.2704299.5484
42.24981.8482-1.29710.9476-0.35891.38930.1715-0.07770.51110.163-0.05150.350.14250.0598-0.00030.8308-0.04090.07080.75110.21011.1026-1.789-8.7304327.8908
51.4785-0.0321-0.09252.5468-0.21652.2019-0.09240.1233-0.0477-0.11480.09790.05890.25330.2126-0.00010.82070.0384-0.0130.6044-0.05910.790944.6087-14.2498273.5966
60.41840.0532-0.16440.4573-0.36590.4789-0.36770.8871-0.0567-0.44710.6854-0.5053-0.70350.3995-0.00070.9671-0.1598-0.03251.2064-0.35061.229775.65775.8709276.1622
70.1443-0.14120.11170.8121-0.12520.6163-0.36972.5332-2.0322-0.26961.4278-1.6005-0.69690.79030.24070.8321-0.10140.20993.0288-1.58362.423189.9301-4.7579266.0157
8-0.07410.32910.23340.22490.47530.4660.27340.898-0.5362-0.25460.5126-0.21471.30380.782202.2694-0.08320.17213.5532-1.10182.539883.7636-12.7124236.2333
91.9045-0.45330.96342.2192-0.20222.2330.15240.0810.1347-0.0042-0.0533-0.11610.0843-0.05550.00010.3965-0.10010.050.49630.01250.524751.932128.5014287.5896
101.34611.05450.14031.941-0.19971.008-0.58910.52520.2511-0.99120.54480.3394-0.1012-0.0148-0.00451.271-0.2634-0.24070.73550.10750.775142.794331.6729245.3545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 302 )D1 - 302
2X-RAY DIFFRACTION2chain 'D' and (resid 303 through 771 )D303 - 771
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 302 )A1 - 302
4X-RAY DIFFRACTION4chain 'A' and (resid 303 through 771 )A303 - 771
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 324 )B1 - 324
6X-RAY DIFFRACTION6chain 'B' and (resid 325 through 411 )B325 - 411
7X-RAY DIFFRACTION7chain 'B' and (resid 412 through 554 )B412 - 554
8X-RAY DIFFRACTION8chain 'B' and (resid 555 through 771 )B555 - 771
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 302 )C1 - 302
10X-RAY DIFFRACTION10chain 'C' and (resid 303 through 771 )C303 - 771

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