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- PDB-5zmm: Structure of the Type IV phosphorothioation-dependent restriction... -

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Basic information

Entry
Database: PDB / ID: 5zmm
TitleStructure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA
ComponentsUncharacterized protein McrA
KeywordsDNA BINDING PROTEIN / Type IV restriction endonuclease / DNA Phosphorothioation
Function / homologyHNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / zinc ion binding / HNH nuclease domain-containing protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.15 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

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Assembly

Deposited unit
A: Uncharacterized protein McrA
B: Uncharacterized protein McrA
C: Uncharacterized protein McrA
D: Uncharacterized protein McrA
E: Uncharacterized protein McrA
F: Uncharacterized protein McrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,51323
Polymers373,0646
Non-polymers1,44917
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17260 Å2
ΔGint-240 kcal/mol
Surface area140350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.183, 139.367, 281.005
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
Uncharacterized protein McrA


Mass: 62177.262 Da / Num. of mol.: 6
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium sulfate, 0.1M Tris-HCl, pH 8.5, 13% (w/v) polyethylene glycol (PEG) 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.15→140.5 Å / Num. obs: 88897 / % possible obs: 99.9 % / Redundancy: 5.7 % / Net I/σ(I): 12.8
Reflection shellResolution: 3.15→3.26 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 3.15→140.5 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.855 / SU B: 21.417 / SU ML: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.522
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 3796 4.8 %RANDOM
Rwork0.245 ---
obs0.2467 74915 88.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 198.7 Å2 / Biso mean: 69.705 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--0.6 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 3.15→140.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23267 0 61 24 23352
Biso mean--60.81 22.39 -
Num. residues----3029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01923877
X-RAY DIFFRACTIONr_bond_other_d0.0070.0221822
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9632496
X-RAY DIFFRACTIONr_angle_other_deg1.034350288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.14853001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.49322.9951105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.934153643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.20315233
X-RAY DIFFRACTIONr_chiral_restr0.0850.23501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02127009
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025042
LS refinement shellResolution: 3.149→3.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 114 -
Rwork0.312 2222 -
all-2336 -
obs--35.6 %

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