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- PDB-5zmn: Sulfur binding domain and SRA domain of ScoMcrA complexed with ph... -

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Basic information

Entry
Database: PDB / ID: 5zmn
TitleSulfur binding domain and SRA domain of ScoMcrA complexed with phosphorothioated DNA
Components
  • DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')
  • Uncharacterized protein McrA
KeywordsDNA BINDING PROTEIN/DNA / Type IV restriction endonuclease / DNA Phosphorothioation / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyHNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / zinc ion binding / DNA / HNH nuclease domain-containing protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.29 Å
AuthorsLiu, G. / Fu, W. / Zhang, Z. / He, Y. / Yu, H. / Zhao, Y. / Deng, Z. / Wu, G. / He, X.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation (China)31670034 China
National Science Foundation (China)31470223 China
National Science Foundation (China)31670106 China
National Science Foundation (China)31130068 China
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for the recognition of sulfur in phosphorothioated DNA.
Authors: Liu, G. / Fu, W. / Zhang, Z. / He, Y. / Yu, H. / Wang, Y. / Wang, X. / Zhao, Y. / Deng, Z. / Wu, G. / He, X.
History
DepositionApr 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / 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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein McrA
B: DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')
C: DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0157
Polymers45,6303
Non-polymers3844
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-50 kcal/mol
Surface area17910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.340, 122.340, 313.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Uncharacterized protein McrA


Mass: 39504.258 Da / Num. of mol.: 1 / Fragment: SBD-SRA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO4631 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L0M9
#2: DNA chain DNA (5'-D(*CP*CP*CP*GP*(GS)P*CP*CP*GP*GP*G)-3')


Mass: 3063.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces lividans (bacteria)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 6.43 Å3/Da / Density % sol: 80.87 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 2.0M ammonium sulfate, 0.1M CAPS buffer, pH 10.5, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 3.29→113.98 Å / Num. obs: 34877 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 14.1
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 3.29→113.98 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.821 / SU B: 20.896 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.595 / ESU R Free: 0.394
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2878 943 5.1 %RANDOM
Rwork0.2507 ---
obs0.2526 17670 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 213.46 Å2 / Biso mean: 116.972 Å2 / Biso min: 50 Å2
Baniso -1Baniso -2Baniso -3
1-3.78 Å2-0 Å20 Å2
2--3.78 Å2-0 Å2
3----7.55 Å2
Refinement stepCycle: final / Resolution: 3.29→113.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 404 20 3 2950
Biso mean--125.79 75.57 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0183061
X-RAY DIFFRACTIONr_bond_other_d0.0070.022581
X-RAY DIFFRACTIONr_angle_refined_deg1.7921.8284253
X-RAY DIFFRACTIONr_angle_other_deg1.21635953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.325323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.93522.742124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.93515388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7021527
X-RAY DIFFRACTIONr_chiral_restr0.1120.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213196
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02689
LS refinement shellResolution: 3.285→3.37 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 74 -
Rwork0.381 1243 -
all-1317 -
obs--97.34 %

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