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

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Basic information

Entry
Database: PDB / ID: 7ccj
TitleSulfur binding domain of SprMcrA complexed with phosphorothioated DNA
Components
  • (DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')) x 2
  • HNHc domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / sulfur binding domain / restriction enzyme / phosphorothioated DNA / 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 / Uncharacterized protein
Function and homology information
Biological speciesStreptomyces pristinaespiralis (bacteria)
Bermanella marisrubri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 17, 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
E: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
B: HNHc domain-containing protein
C: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
D: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)46,3166
Polymers46,3166
Non-polymers00
Water0
1
A: HNHc domain-containing protein
E: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
F: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)23,1583
Polymers23,1583
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-11 kcal/mol
Surface area9450 Å2
MethodPISA
2
B: HNHc domain-containing protein
C: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')
D: DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)23,1583
Polymers23,1583
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-10 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.729, 105.279, 116.414
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C
21chain E
12chain D
22chain F
13(chain A and (resid 4 through 43 or (resid 44...
23(chain B and (resid 4 through 129 or (resid 130...

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
111DGDGDCDCchain CCE1 - 81 - 8
211DGDGDCDCchain EEB1 - 81 - 8
112DGDGDCDCchain DDF1 - 81 - 8
212DGDGDCDCchain FFC1 - 81 - 8
113THRTHRALAALA(chain A and (resid 4 through 43 or (resid 44...AA4 - 434 - 43
123ARGARGARGARG(chain A and (resid 4 through 43 or (resid 44...AA4444
133THRTHRTYRTYR(chain A and (resid 4 through 43 or (resid 44...AA4 - 1624 - 162
143THRTHRTYRTYR(chain A and (resid 4 through 43 or (resid 44...AA4 - 1624 - 162
153THRTHRTYRTYR(chain A and (resid 4 through 43 or (resid 44...AA4 - 1624 - 162
163THRTHRTYRTYR(chain A and (resid 4 through 43 or (resid 44...AA4 - 1624 - 162
213THRTHRHISHIS(chain B and (resid 4 through 129 or (resid 130...BD4 - 1294 - 129
223ARGARGARGARG(chain B and (resid 4 through 129 or (resid 130...BD130130
233THRTHRGLUGLU(chain B and (resid 4 through 129 or (resid 130...BD4 - 1644 - 164
243THRTHRGLUGLU(chain B and (resid 4 through 129 or (resid 130...BD4 - 1644 - 164
253THRTHRGLUGLU(chain B and (resid 4 through 129 or (resid 130...BD4 - 1644 - 164
263THRTHRGLUGLU(chain B and (resid 4 through 129 or (resid 130...BD4 - 1644 - 164

NCS ensembles :
ID
1
2
3

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Components

#1: Protein HNHc domain-containing protein


Mass: 18288.637 Da / Num. of mol.: 2 / 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
#2: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bermanella marisrubri (bacteria)
#3: DNA chain DNA (5'-D(*GP*GP*AP*TP*CP*AP*TP*C)-3')


Mass: 2442.682 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bermanella marisrubri (bacteria)
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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Tris-HCl pH 8.5, PEG 8000

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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: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 9347 / % possible obs: 100 % / Redundancy: 13.1 % / Biso Wilson estimate: 71.31 Å2 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.129 / Rrim(I) all: 0.468 / Χ2: 0.616 / Net I/σ(I): 1.2 / Num. measured all: 122806
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.3-3.4213.91.5519230.9080.431.610.494100
3.42-3.5513.20.9818980.9480.2861.0230.75899.9
3.55-3.7213.70.9489180.9460.2680.9860.585100
3.72-3.9113.40.8559290.9620.2480.8910.649100
3.91-4.1613.30.5779140.9890.1640.60.546100
4.16-4.48130.4279420.9820.1220.4450.569100
4.48-4.9311.70.3419250.9890.1030.3560.581100
4.93-5.6413.90.3689370.9870.1020.3820.56100
5.64-7.113.40.2859530.9880.080.2960.561100
7.1-50120.13210080.9950.040.1380.87499.7

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZMO

5zmo


Resolution: 3.3→28.726 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 36.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 437 4.77 %
Rwork0.241 8729 -
obs0.2435 9166 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.28 Å2 / Biso mean: 62.1251 Å2 / Biso min: 32.56 Å2
Refinement stepCycle: final / Resolution: 3.3→28.726 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 650 0 0 3090
Num. residues----352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033230
X-RAY DIFFRACTIONf_angle_d0.6274522
X-RAY DIFFRACTIONf_chiral_restr0.037500
X-RAY DIFFRACTIONf_plane_restr0.004482
X-RAY DIFFRACTIONf_dihedral_angle_d14.8231776
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C152X-RAY DIFFRACTION9.454TORSIONAL
12E152X-RAY DIFFRACTION9.454TORSIONAL
21D128X-RAY DIFFRACTION9.454TORSIONAL
22F128X-RAY DIFFRACTION9.454TORSIONAL
31A1436X-RAY DIFFRACTION9.454TORSIONAL
32B1436X-RAY DIFFRACTION9.454TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3-3.77630.29871540.2662286799
3.7763-4.75420.27761400.2235290299
4.7542-28.7260.3021430.2413296098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5107-1.63350.30741.67881.42163.54780.1419-0.06310.02910.3590.10050.10610.03980.2501-0.22790.4809-0.0761-0.00820.30520.04110.3927-12.436-8.485-13.044
24.6714-0.39160.90392.7677-0.22.24290.2227-0.27850.10960.2505-0.0748-0.4482-0.22740.2256-0.12320.5676-0.0498-0.01560.33690.07070.5108-36.649-34.022-12.865
35.5978-2.15610.79315.6386-1.03242.6133-0.0027-0.22751.41560.0894-0.644-1.05270.2418-0.12620.53460.7016-0.0247-0.05470.5981-0.14020.6733-23.725-34.422-31.849
44.75131.44810.0723.57483.50983.8239-0.21110.0599-0.3095-0.9565-0.0953-0.02280.29860.26140.36760.63870.0202-0.07130.4039-0.07310.3631-25.284-34.11-27.884
52.97050.08783.60934.9365-4.04747.88850.3689-0.6147-1.2327-0.2650.10051.88540.7975-0.578-0.52940.8815-0.1028-0.07050.6509-0.02450.6782-25.05-8.212-32.164
62.9248-1.4051-1.4733.637-3.82387.90260.0042-0.53320.1215-1.0488-0.18640.06431.67810.06320.11480.56210.0031-0.28490.52940.04850.5897-23.66-8.554-28.18
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:162 )A4 - 162
2X-RAY DIFFRACTION2( CHAIN B AND RESID 4:164 )B4 - 164
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1:8 )C1 - 8
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:8 )D1 - 8
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1:8 )E1 - 8
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:8 )F1 - 8

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