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- PDB-5zmo: Sulfur binding domain of ScoMcrA complexed with phosphorothioated DNA -

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Basic information

Entry
Database: PDB / ID: 5zmo
TitleSulfur binding domain of ScoMcrA complexed with phosphorothioated DNA
Components
  • DNA (5'-D(P*CP*CP*GP*(GS)P*CP*CP*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 / homology
Function and homology information


endonuclease activity / nucleic acid binding / zinc ion binding
Similarity search - Function
HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease
Similarity search - Domain/homology
PHOSPHATE ION / DNA / HNH nuclease domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
Streptomyces lividans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.69 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(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3')
C: DNA (5'-D(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2966
Polymers24,0113
Non-polymers2853
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-8 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.022, 57.148, 42.320
Angle α, β, γ (deg.)90.000, 101.350, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Uncharacterized protein McrA


Mass: 19121.752 Da / Num. of mol.: 1 / Fragment: SBD 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(P*CP*CP*GP*(GS)P*CP*CP*GP*G)-3') / PT-DNA


Mass: 2444.659 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces lividans (bacteria)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.35 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES, pH 7.5, 0.8M ammonium phosphate monobasic, 0.8M potassium phosphate monobasic, 1% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 22244 / % possible obs: 97 % / Redundancy: 3.8 % / Net I/σ(I): 11.4
Reflection shellResolution: 1.7→1.76 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
RefinementResolution: 1.69→47.65 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.944 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 1101 4.9 %RANDOM
Rwork0.1881 ---
obs0.1901 21142 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.45 Å2 / Biso mean: 31.482 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å2-0.15 Å2
2--5.31 Å20 Å2
3----2.23 Å2
Refinement stepCycle: final / Resolution: 1.69→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 287 15 99 1640
Biso mean--59.59 36.03 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0181624
X-RAY DIFFRACTIONr_bond_other_d0.0020.021373
X-RAY DIFFRACTIONr_angle_refined_deg1.8881.8032270
X-RAY DIFFRACTIONr_angle_other_deg1.24133165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.84521.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58115200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0881517
X-RAY DIFFRACTIONr_chiral_restr0.1410.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211632
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02360
LS refinement shellResolution: 1.691→1.735 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 83 -
Rwork0.252 1387 -
all-1470 -
obs--88.82 %

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