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- PDB-7drr: Structure of SspE-R100A protein -

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Basic information

Entry
Database: PDB / ID: 7drr
TitleStructure of SspE-R100A protein
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: 3.48 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)348,2454
Polymers348,2454
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13710 Å2
ΔGint-44 kcal/mol
Surface area125030 Å2
Unit cell
Length a, b, c (Å)110.028, 137.970, 292.354
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: 87061.234 Da / Num. of mol.: 4 / Fragment: DUF262 and DUF1524 domains / Mutation: R100A
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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 3350, 4% Tacsimate 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: Nov 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.48→50 Å / Num. obs: 56714 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 0.988 / Net I/σ(I): 2
Reflection shellResolution: 3.48→3.56 Å / Num. unique obs: 2809 / CC1/2: 0.583

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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: 3.48→36.54 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 2715 5.02 %
Rwork0.224 --
obs0.2276 54046 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 213.66 Å2 / Biso mean: 79.4183 Å2 / Biso min: 3.54 Å2
Refinement stepCycle: final / Resolution: 3.48→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24524 0 0 0 24524
Num. residues----3084
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A14353X-RAY DIFFRACTION7.305TORSIONAL
12B14353X-RAY DIFFRACTION7.305TORSIONAL
13C14353X-RAY DIFFRACTION7.305TORSIONAL
14D14353X-RAY DIFFRACTION7.305TORSIONAL
LS refinement shellResolution: 3.48→3.54 Å
RfactorNum. reflection% reflection
Rfree0.3699 --
Rwork0.314 --
obs-2809 85.8 %
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)
10.20630.0045-0.13860.23550.06960.16880.0393-0.3769-0.08090.349-0.0038-0.03870.11620.27060.1608-0.04960.08-0.1590.23580.1623-0.166545.882219.0841316.3157
2-0.0297-0.02110.07390.0941-0.09670.12010.2293-0.1443-0.0060.239-0.2938-0.0449-0.00250.35330.1230.4037-0.2717-0.10090.59020.55080.045148.9459-9.774348.1801
30.1554-0.0106-0.03510.11050.05210.0911-0.087-0.0806-0.12460.0726-0.06060.04660.3398-0.1385-0.21630.3717-0.13-0.02270.17410.27920.345427.5355-19.3427298.9252
40.07560.03640.05230.19590.13480.16810.24430.17620.48480.12090.05340.13060.1584-0.21960.2380.2448-0.2070.18670.2720.7050.7822-3.8236-8.7692327.9532
50.04930.00740.01230.16060.04730.1637-0.0350.0577-0.1099-0.14840.1167-0.2470.1280.356-0.04370.106-0.0686-0.0846-0.1232-0.24670.234149.6847-10.5371272.6119
60.0688-0.0315-0.05410.01570.01410.08460.06090.11370.012-0.19030.0697-0.0850.11440.0460.17830.55330.09910.09180.7765-0.58970.760684.6831-10.1683247.8925
70.16150.09170.00040.26130.00360.15190.0260.1209-0.0714-0.07060.0792-0.09120.069-0.1620.4014-0.4802-0.18-0.01540.0526-0.01710.052551.890927.055286.0845
8-0.01560.05350.01790.04980.00570.0696-0.03520.1980.2392-0.36250.08980.0468-0.26390.09180.33160.442-0.2925-0.40930.1735-0.0322-0.034141.68232.9587242.4508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 301 )D1 - 301
2X-RAY DIFFRACTION2chain 'D' and (resid 302 through 771 )D302 - 771
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 324 )A1 - 324
4X-RAY DIFFRACTION4chain 'A' and (resid 325 through 771 )A325 - 771
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 399 )B1 - 399
6X-RAY DIFFRACTION6chain 'B' and (resid 400 through 771 )B400 - 771
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 324 )C1 - 324
8X-RAY DIFFRACTION8chain 'C' and (resid 325 through 771 )C325 - 771

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