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- PDB-7cc9: Sulfur binding domain of SprMcrA complexed with phosphorothioated DNA -

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Basic information

Entry
Database: PDB / ID: 7cc9
TitleSulfur binding domain of SprMcrA complexed with phosphorothioated DNA
Components
  • DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
  • DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
  • HNHc domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / sulfur binding domain / restriction enzyme / phosphorothioated DNA / 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
ACETATE ION / DNA / HNH endonuclease
Similarity search - Component
Biological speciesStreptomyces pristinaespiralis (bacteria)
Streptomyces lividans 1326 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.063 Å
AuthorsYu, H. / Zhao, G. / Gan, J. / Liu, G. / Wu, G. / He, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670034 China
National Natural Science Foundation of China (NSFC)31470195 China
National Natural Science Foundation of China (NSFC)21661140002 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses.
Authors: Yu, H. / Li, J. / Liu, G. / Zhao, G. / Wang, Y. / Hu, W. / Deng, Z. / Wu, G. / Gan, J. / Zhao, Y.L. / He, X.
History
DepositionJun 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: HNHc domain-containing protein
B: HNHc domain-containing protein
C: HNHc domain-containing protein
D: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
E: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
G: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
H: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
I: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,22325
Polymers68,8019
Non-polymers1,42216
Water6,756375
1
A: HNHc domain-containing protein
D: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
E: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,56510
Polymers22,9343
Non-polymers6317
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HNHc domain-containing protein
F: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
G: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,62811
Polymers22,9343
Non-polymers6948
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HNHc domain-containing protein
H: DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')
I: DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0304
Polymers22,9343
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.496, 154.496, 156.802
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 3 and (name C or name...
21(chain B and (resid 3 through 5 or (resid 6...
31(chain C and ((resid 3 and (name C or name...
12chain E
22chain G
32chain I
13chain D
23chain F
33chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEULEULEU(chain A and ((resid 3 and (name C or name...AA31
121LEULEUGLYGLY(chain A and ((resid 3 and (name C or name...AA3 - 1651 - 163
211LEULEUASPASP(chain B and (resid 3 through 5 or (resid 6...BB3 - 51 - 3
221THRTHRASPASP(chain B and (resid 3 through 5 or (resid 6...BB6 - 74 - 5
231LEULEUGLYGLY(chain B and (resid 3 through 5 or (resid 6...BB3 - 1651 - 163
311LEULEULEULEU(chain C and ((resid 3 and (name C or name...CC31
321LEULEUGLYGLY(chain C and ((resid 3 and (name C or name...CC3 - 1651 - 163
112DGDGDCDCchain EEE1 - 81 - 8
212DGDGDCDCchain GGG1 - 81 - 8
312DGDGDCDCchain III1 - 81 - 8
113DGDGDCDCchain DDD1 - 81 - 8
213DGDGDCDCchain FFF1 - 81 - 8
313DGDGDCDCchain HHH1 - 81 - 8

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein HNHc domain-containing protein


Mass: 18060.322 Da / Num. of mol.: 3 / Fragment: Sulfur binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria)
Gene: SPRI_5136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M4DML1

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DNA chain , 2 types, 6 molecules DFHEGI

#2: DNA chain DNA (5'-D(*GP*GP*CP*GP*GS*CP*CP*C)-3')


Mass: 2444.659 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Streptomyces lividans 1326 (bacteria)
#3: DNA chain DNA (5'-D(*GP*GP*GP*CP*CP*GP*CP*C)-3')


Mass: 2428.593 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Streptomyces lividans 1326 (bacteria)

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Non-polymers , 4 types, 391 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.89 Å3/Da / Density % sol: 68.38 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: magnesium actate tetrahydrate, sodium cacodylate trihydrate, lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 68202 / % possible obs: 100 % / Redundancy: 38.3 % / Biso Wilson estimate: 27.61 Å2 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.024 / Rrim(I) all: 0.144 / Χ2: 1.101 / Net I/σ(I): 6.5 / Num. measured all: 2611102
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.06-2.1329.82.47767030.5120.4632.521.355
2.13-2.22361.95367170.7870.3281.9811.022
2.22-2.3237.41.19866990.890.1971.2141.216
2.32-2.4441.10.79867460.9610.1250.8081.039
2.44-2.640.80.48567320.9850.0760.4911.042
2.6-2.838.80.2867850.9930.0450.2841.075
2.8-3.0840.70.17767960.9950.0280.1790.975
3.08-3.5240.40.11368510.9980.0180.1140.921
3.52-4.4439.90.11469150.9960.0180.1161.015
4.44-5037.80.1372580.9270.0230.1321.423

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZMO

5zmo


Resolution: 2.063→48.684 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 3053 4.98 %
Rwork0.2108 58228 -
obs0.2119 61281 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.15 Å2 / Biso mean: 36.1237 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 2.063→48.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 966 78 375 5167
Biso mean--69.83 37.1 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034989
X-RAY DIFFRACTIONf_angle_d0.6896961
X-RAY DIFFRACTIONf_chiral_restr0.043750
X-RAY DIFFRACTIONf_plane_restr0.004746
X-RAY DIFFRACTIONf_dihedral_angle_d16.0232961
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2213X-RAY DIFFRACTION10.607TORSIONAL
12B2213X-RAY DIFFRACTION10.607TORSIONAL
13C2213X-RAY DIFFRACTION10.607TORSIONAL
21E228X-RAY DIFFRACTION10.607TORSIONAL
22G228X-RAY DIFFRACTION10.607TORSIONAL
23I228X-RAY DIFFRACTION10.607TORSIONAL
31D189X-RAY DIFFRACTION10.607TORSIONAL
32F189X-RAY DIFFRACTION10.607TORSIONAL
33H189X-RAY DIFFRACTION10.607TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.063-2.09490.3536530.32283429
2.0949-2.12920.3144510.2905109638
2.1292-2.16590.3462910.2638146351
2.1659-2.20530.26961120.2821205071
2.2053-2.24770.31251250.2836266391
2.2477-2.29360.26071490.2741280897
2.2936-2.34350.30241470.26022915100
2.3435-2.3980.26121340.25792890100
2.398-2.4580.2841530.23892922100
2.458-2.52440.27531490.23412916100
2.5244-2.59870.25551560.23392884100
2.5987-2.68260.25441610.23432924100
2.6826-2.77840.25371610.23872906100
2.7784-2.88970.27641430.24412935100
2.8897-3.02120.27981420.25112964100
3.0212-3.18040.25691540.23152938100
3.1804-3.37960.21871500.1979294399
3.3796-3.64050.19811490.18062962100
3.6405-4.00670.21621660.17532976100
4.0067-4.58610.15821530.14843008100
4.5861-5.77650.19041760.1693021100
5.7765-48.6840.20281780.20283210100
Refinement TLS params.Method: refined / Origin x: 61.2856 Å / Origin y: -27.1001 Å / Origin z: 9.752 Å
111213212223313233
T0.3567 Å20.0432 Å20.011 Å2-0.0538 Å2-0.002 Å2--0.1706 Å2
L0.771 °20.0147 °20.0352 °2-0.2944 °20.0666 °2--0.8317 °2
S0.0074 Å °-0.0367 Å °0.0107 Å °0.128 Å °0.0783 Å °0.0404 Å °0.2258 Å °0.074 Å °-0.0752 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 165
2X-RAY DIFFRACTION1allB3 - 165
3X-RAY DIFFRACTION1allC3 - 165
4X-RAY DIFFRACTION1allD1 - 8
5X-RAY DIFFRACTION1allE1 - 8
6X-RAY DIFFRACTION1allF1 - 8
7X-RAY DIFFRACTION1allG1 - 8
8X-RAY DIFFRACTION1allH1 - 8
9X-RAY DIFFRACTION1allI1 - 8
10X-RAY DIFFRACTION1allJ1 - 15
11X-RAY DIFFRACTION1allK1 - 2
12X-RAY DIFFRACTION1allK3
13X-RAY DIFFRACTION1allS1 - 583
14X-RAY DIFFRACTION1allL1

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