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- PDB-6jiv: SspE crystal structure -

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Basic information

Entry
Database: PDB / ID: 6jiv
TitleSspE crystal structure
ComponentsSspE protein
KeywordsHYDROLASE / DNase / PT
Biological speciesStreptomyces yokosukanensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.31 Å
AuthorsBing, Y.Z. / Yang, H.G.
CitationJournal: Nat Microbiol / Year: 2020
Title: SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities.
Authors: Xiong, X. / Wu, G. / Wei, Y. / Liu, L. / Zhang, Y. / Su, R. / Jiang, X. / Li, M. / Gao, H. / Tian, X. / Zhang, Y. / Hu, L. / Chen, S. / Tang, Y. / Jiang, S. / Huang, R. / Li, Z. / Wang, Y. / ...Authors: Xiong, X. / Wu, G. / Wei, Y. / Liu, L. / Zhang, Y. / Su, R. / Jiang, X. / Li, M. / Gao, H. / Tian, X. / Zhang, Y. / Hu, L. / Chen, S. / Tang, Y. / Jiang, S. / Huang, R. / Li, Z. / Wang, Y. / Deng, Z. / Wang, J. / Dedon, P.C. / Chen, S. / Wang, L.
History
DepositionFeb 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)351,2164
Polymers351,2164
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11540 Å2
ΔGint-36 kcal/mol
Surface area108420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.070, 138.160, 293.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SspE protein


Mass: 87803.883 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces yokosukanensis (bacteria)
Has ligand of interestN
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: 3.21 Å3/Da / Density % sol: 61.66 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns.
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG MME 5000, HEPES pH 7.0, Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 3.31→125.33 Å / Num. obs: 64318 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 8.58
Reflection shellResolution: 3.3→3.5 Å / Num. unique obs: 52096 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.31→125.33 Å / Cor.coef. Fo:Fc: 0.802 / Cor.coef. Fo:Fc free: 0.76 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.678 / ESU R Free: 0.711 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.435 3357 5 %RANDOM
Rwork0.4063 ---
obs0.4078 64318 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 346.76 Å2 / Biso mean: 99.711 Å2 / Biso min: 29.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å20 Å20 Å2
2--5.53 Å2-0 Å2
3----3.78 Å2
Refinement stepCycle: final / Resolution: 3.31→125.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15090 0 0 0 15090
Num. residues----2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01315290
X-RAY DIFFRACTIONr_bond_other_d0.0380.01714611
X-RAY DIFFRACTIONr_angle_refined_deg2.4961.62420907
X-RAY DIFFRACTIONr_angle_other_deg2.5741.5633225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.67952221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15121.244595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.063151731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3981593
X-RAY DIFFRACTIONr_chiral_restr0.1090.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218317
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023290
LS refinement shellResolution: 3.313→3.399 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 226 -
Rwork0.411 4477 -
all-4703 -
obs--94.78 %

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