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- PDB-6s58: AvaII restriction endonuclease in the absence of nucleic acids -

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Basic information

Entry
Database: PDB / ID: 6s58
TitleAvaII restriction endonuclease in the absence of nucleic acids
ComponentsType II site-specific deoxyribonuclease
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / APO / SCANNING / SUBSTRATE / PRODUCT COMPLEX / RNA/DNA HYBRID / RNA/DNA HETERODUPLEX / A-DNA
Function / homologyType II restriction endonuclease SinI / SinI restriction endonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding / Type II site-specific deoxyribonuclease
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKisiala, M. / Kowalska, M. / Korza, H. / Czapinska, H. / Bochtler, M.
Citation
Journal: Nucleic Acids Res. / Year: 2020
Title: Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation.
Authors: Kisiala, M. / Kowalska, M. / Pastor, M. / Korza, H.J. / Czapinska, H. / Bochtler, M.
#1: Journal: Nucleic Acids Res. / Year: 2010
Title: Sequence-specific cleavage of RNA by Type II restriction enzymes.
Authors: Murray, I.A. / Stickel, S.K. / Roberts, R.J.
#2: Journal: Nucleic Acids Res. / Year: 1980
Title: Cleavage of DNA.RNA hybrids by type II restriction enzymes.
Authors: Molloy, P.L. / Symons, R.H.
#3: Journal: J. Biol. Chem. / Year: 2005
Title: Crystal structures of type II restriction endonuclease EcoO109I and its complex with cognate DNA.
Authors: Hashimoto, H. / Shimizu, T. / Imasaki, T. / Kato, M. / Shichijo, N. / Kita, K. / Sato, M.
#4: Journal: Biophys. J. / Year: 2009
Title: Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics simulations and X-ray scattering data analysis.
Authors: Oroguchi, T. / Hashimoto, H. / Shimizu, T. / Sato, M. / Ikeguchi, M.
History
DepositionJun 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II site-specific deoxyribonuclease
B: Type II site-specific deoxyribonuclease
C: Type II site-specific deoxyribonuclease
D: Type II site-specific deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,88310
Polymers108,6474
Non-polymers2366
Water1,74797
1
A: Type II site-specific deoxyribonuclease
B: Type II site-specific deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4395
Polymers54,3242
Non-polymers1163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-51 kcal/mol
Surface area23450 Å2
MethodPISA
2
C: Type II site-specific deoxyribonuclease
D: Type II site-specific deoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4445
Polymers54,3242
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-64 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.231, 102.733, 121.197
Angle α, β, γ (deg.)90.00, 90.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Type II site-specific deoxyribonuclease / AvaII restriction endonuclease


Mass: 27161.797 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Gene: alr0933 / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Variant (production host): ER2566 / References: UniProt: Q8YYB7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03 M CaCl2, 0.1 M MES/imidazole, pH 6.5, 12.5% v/v MPD, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350 (Morpheus screen A4 condition with MgCl2 eliminated).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.694
11-h,-k,l20.306
ReflectionResolution: 2.35→53.3 Å / Num. obs: 37373 / % possible obs: 99.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 54 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.065 / Rrim(I) all: 0.119 / Net I/σ(I): 5.5
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3687 / CC1/2: 0.764 / Rpim(I) all: 0.309 / Rrim(I) all: 0.55 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3B

6g3b


Resolution: 2.32→51.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.9 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25827 1958 5.3 %RANDOM
Rwork0.21634 ---
obs0.21848 35320 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.422 Å2
Baniso -1Baniso -2Baniso -3
1-16.22 Å20 Å27.04 Å2
2---30.14 Å2-0 Å2
3---13.92 Å2
Refinement stepCycle: LAST / Resolution: 2.32→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7252 0 6 97 7355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197431
X-RAY DIFFRACTIONr_bond_other_d0.0010.026902
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.95110041
X-RAY DIFFRACTIONr_angle_other_deg0.886316073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5815900
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7124.232345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925151341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5721546
X-RAY DIFFRACTIONr_chiral_restr0.0640.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8257.1523615
X-RAY DIFFRACTIONr_mcbond_other2.8257.1513614
X-RAY DIFFRACTIONr_mcangle_it4.40610.7184510
X-RAY DIFFRACTIONr_mcangle_other4.40510.724511
X-RAY DIFFRACTIONr_scbond_it2.5477.3683815
X-RAY DIFFRACTIONr_scbond_other2.5477.3693816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.10510.9565532
X-RAY DIFFRACTIONr_long_range_B_refined6.52581.7748368
X-RAY DIFFRACTIONr_long_range_B_other6.49681.7748352
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.324→2.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 90 -
Rwork0.312 1480 -
obs--55.58 %

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