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- PDB-6juf: SspB crystal structure -

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Basic information

Entry
Database: PDB / ID: 6juf
TitleSspB crystal structure
ComponentsSspB protein
KeywordsHYDROLASE / DNase / PT
Function / homologyDomain of unknown function DUF4007 / Protein of unknown function (DUF4007) / DUF4007 domain-containing protein
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.587 Å
AuthorsLiqiong, L. / Yubing, Z.
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
DepositionApr 13, 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 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high / _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

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Assembly

Deposited unit
B: SspB protein
A: SspB protein


Theoretical massNumber of molelcules
Total (without water)82,4972
Polymers82,4972
Non-polymers00
Water8,053447
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.398, 81.637, 148.004
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
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 4 - 351 / Label seq-ID: 4 - 351

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.029813, -0.05794, -0.997875), (-0.117682, -0.991579, 0.054059), (-0.992604, 0.11582, -0.036381)-30.99823, 52.03013, -36.40803

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Components

#1: Protein SspB protein


Mass: 41248.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Streptomyces clavuligerus (strain ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602) (bacteria)
Strain: ATCC 27064 / DSM 738 / JCM 4710 / NBRC 13307 / NCIMB 12785 / NRRL 3585 / VKM Ac-602
References: UniProt: B5GPM3
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 25% polyethyleneglycol (PEG) 3350, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.587→75 Å / Num. obs: 93617 / % possible obs: 98.8 % / Redundancy: 7.3 % / CC1/2: 0.862 / Net I/σ(I): 18
Reflection shellResolution: 1.75→1.84 Å / Num. unique obs: 93617 / CC1/2: 0.954

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.587→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.04 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2384 4616 5 %RANDOM
Rwork0.1925 ---
obs0.1948 87603 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.07 Å2 / Biso mean: 17.843 Å2 / Biso min: 3.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.587→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 0 447 5901
Biso mean---24.03 -
Num. residues----684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195629
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9427658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08722.464276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.65615878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0191557
X-RAY DIFFRACTIONr_chiral_restr0.1360.2802
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214415
X-RAY DIFFRACTIONr_rigid_bond_restr8.535629
X-RAY DIFFRACTIONr_sphericity_free19.1955130
X-RAY DIFFRACTIONr_sphericity_bonded11.24755790
Refine LS restraints NCS

Ens-ID: 1 / Number: 409 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.587→1.628 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.268 287 -
Rwork0.209 5389 -
obs--85.16 %

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