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- PDB-6lb9: Magnesium ion-bound SspB crystal structure -

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Basic information

Entry
Database: PDB / ID: 6lb9
TitleMagnesium ion-bound SspB crystal structure
ComponentsDUF4007 domain-containing 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: 2.227 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
DepositionNov 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF4007 domain-containing protein
B: DUF4007 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5454
Polymers82,4972
Non-polymers492
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-18 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.248, 80.249, 146.022
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 DUF4007 domain-containing protein / SspB protein


Mass: 41248.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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
Gene: SCLAV_2519, SSCG_01550 / Production host: Escherichia coli (E. coli) / References: UniProt: B5GPM3
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350,0.2M Magnesium chloride

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 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: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.22→73.01 Å / Num. obs: 33730 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.992 / Net I/σ(I): 8.5
Reflection shellResolution: 2.22→2.3 Å / Num. unique obs: 30780 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.227→46.605 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 1633 5.04 %RANDOM
Rwork0.1958 30776 --
obs0.1987 32409 96.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.35 Å2 / Biso mean: 31.5671 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 2.227→46.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 0 2 159 5637
Biso mean--30.71 31.39 -
Num. residues----689
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.227-2.29290.22991300.2074285599
2.2273-2.29290.27881130.1884220683
2.2929-2.36690.30141090.2042235390
2.3669-2.45150.27871260.2142238291
2.4515-2.54960.31911490.2191247895
2.5496-2.66560.27581280.2145261698
2.6656-2.80620.28531310.207261799
2.8062-2.98190.26991150.20782676100
2.9819-3.21210.27141520.20822637100
3.2121-3.53530.23791670.18552629100
3.5353-4.04660.24571610.1761265299
4.0466-5.09730.21871520.1743267599

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