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- PDB-5gkf: Structure of EndoMS-dsDNA1' complex -

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Basic information

Entry
Database: PDB / ID: 5gkf
TitleStructure of EndoMS-dsDNA1' complex
Components
  • DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3')
  • Endonuclease EndoMS
KeywordsHYDROLASE/DNA / ENDONUCLEASE / DNA COMPLEX / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / cytoplasm
Similarity search - Function
Endonuclease NucS / : / : / : / Endonuclease NucS C-terminal domain / Endonuclease NucS N-terminal PH-like domain / tRNA endonuclease-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Endonuclease NucS
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and DevelopmentDrug Discovery and Life Science Research(Platform for Drug Discovery, Informatics and Structural Life Science) Japan
Ministry of Education, Culture, Sports, Science and Technology25280109 Japan
Ministry of Education, Culture, Sports, Science and Technology26242075 Japan
CitationJournal: Structure / Year: 2016
Title: Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease
Authors: Nakae, S. / Hijikata, A. / Tsuji, T. / Yonezawa, K. / Kouyama, K.I. / Mayanagi, K. / Ishino, S. / Ishino, Y. / Shirai, T.
History
DepositionJul 4, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease EndoMS
B: Endonuclease EndoMS
C: DNA (5'-D(*CP*GP*CP*TP*AP*CP*AP*TP*GP*TP*CP*GP*TP*CP*C)-3')
D: DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,00711
Polymers66,3674
Non-polymers6397
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14470 Å2
ΔGint-142 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.440, 92.440, 404.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endonuclease EndoMS / Endonuclease NucS


Mass: 28598.096 Da / Num. of mol.: 2 / Mutation: D165A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: TK1898 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JER9, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules CD

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


Mass: 4520.935 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*AP*CP*GP*AP*CP*TP*TP*GP*TP*AP*GP*CP*G)-3')


Mass: 4650.021 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 42 molecules

#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 3.94 Å3/Da / Density % sol: 68.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M CALCIUM ACETATE, 80 MM SODIUM CACODYLATE, 14.4%(W/V) PEG8000, 20%(W/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 24789 / % possible obs: 93.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 19.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.4 / % possible all: 95.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BSL

5bsl
PDB Unreleased entry


Resolution: 2.8→24.81 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.247 1257 5.09 %
Rwork0.171 --
obs0.175 24695 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 608 42 35 4485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115253
X-RAY DIFFRACTIONf_angle_d1.3847340
X-RAY DIFFRACTIONf_dihedral_angle_d23.4092122
X-RAY DIFFRACTIONf_chiral_restr0.053835
X-RAY DIFFRACTIONf_plane_restr0.007734
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.9120.31641400.22842569X-RAY DIFFRACTION95
2.912-3.04430.30731360.23412546X-RAY DIFFRACTION95
3.0443-3.20450.30611360.20492564X-RAY DIFFRACTION94
3.2045-3.40480.281320.17832573X-RAY DIFFRACTION94
3.4048-3.6670.23421450.15942567X-RAY DIFFRACTION95
3.667-4.03460.20991670.15252562X-RAY DIFFRACTION94
4.0346-4.61510.22491370.13062621X-RAY DIFFRACTION94
4.6151-5.80230.19441180.14842662X-RAY DIFFRACTION93
5.8023-24.81160.27051460.19822774X-RAY DIFFRACTION91

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