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- PDB-6s48: AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA -

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Basic information

Entry
Database: PDB / ID: 6s48
TitleAvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA
Components
  • DNA (5'-D(*GP*AP*TP*G)-3')
  • DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3')
  • DNA (5'-D(*GP*TP*AP*G)-3')
  • DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3')
  • DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3')
  • Type II site-specific deoxyribonuclease
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / DNA COMPLEX / A-DNA / PD-(D/E)XK
Function / homology
Function and homology information


type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding / metal ion binding
Similarity search - Function
Type II restriction endonuclease SinI / SinI restriction endonuclease
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / TRIETHYLENE GLYCOL / SERINE / DNA / DNA (> 10) / Type II site-specific deoxyribonuclease
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 26, 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 / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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: DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*G)-3')
E: DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3')
F: DNA (5'-D(*GP*AP*TP*G)-3')
G: DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3')
H: DNA (5'-D(*GP*TP*AP*G)-3')
I: DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,45419
Polymers67,6049
Non-polymers85010
Water8,773487
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.129, 116.210, 56.774
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27161.797 Da / Num. of mol.: 2
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

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DNA chain , 5 types, 7 molecules CDHEIFG

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


Mass: 3349.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*AP*G)-3')


Mass: 1230.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3')


Mass: 2082.400 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(*GP*AP*TP*G)-3')


Mass: 1230.854 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3')


Mass: 2073.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 497 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H6OS
#9: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#10: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H7NO3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen H1 conditions: 0.02 M of L-Na-glutamate, alanine (racemic), glycine, lysine HCl (racemic), serine (racemic), 0.1 M buffer (1 M Imidazole, 1 M MES, pH 6.5), 30% precipitant ...Details: Morpheus screen H1 conditions: 0.02 M of L-Na-glutamate, alanine (racemic), glycine, lysine HCl (racemic), serine (racemic), 0.1 M buffer (1 M Imidazole, 1 M MES, pH 6.5), 30% precipitant (20% w/v PEG 20 000, 40% v/v PEG MME 550)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→40.07 Å / Num. obs: 36585 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.1 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.094 / Rsym value: 0.081 / Net I/σ(I): 10.55
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.43 / Num. unique obs: 5824 / CC1/2: 0.615 / Rrim(I) all: 0.943 / Rsym value: 0.807 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
BALBESphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G3B

6g3b


Resolution: 1.9→40.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.795 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.166
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ION IDENTITY WAS ASSIGNED TENTATIVELY. THE RESOLUTION OF THE STRUCTURE WAS NOT GOOD ENOUGH FOR ITS EXPERIMENTAL VALIDATION. THE ...Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE ION IDENTITY WAS ASSIGNED TENTATIVELY. THE RESOLUTION OF THE STRUCTURE WAS NOT GOOD ENOUGH FOR ITS EXPERIMENTAL VALIDATION. THE ION IDENTIFICATION THROUGH LONG WAVELENGTH DATA COLLECTION WAS ATTEMPTED BUT THE ANOMALOUS SIGNAL WAS VERY WEAK. THE CYSTEINE MODIFICATION WAS MODELED AS 2-MERCAPTOETHANOL, BUT MAY AS WELL CORRESPOND TO DITHIOTHREITOL. BOTH AGENTS WERE PRESENT AT CERTAIN PURIFICATION STAGES. FREE SERINE FROM THE CRYSTALLIZATION BUFFER WAS MODELED IN THE DENSITY BUT ITS IDENTITY IS VERY UNCERTAIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.21671 1825 5 %RANDOM
Rwork0.17621 ---
obs0.17826 34760 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.854 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0 Å2-0.35 Å2
2---1.27 Å2-0 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3720 893 46 487 5146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0185146
X-RAY DIFFRACTIONr_bond_other_d0.0020.024367
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.7917158
X-RAY DIFFRACTIONr_angle_other_deg0.998310215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95223.874191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31415757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5561529
X-RAY DIFFRACTIONr_chiral_restr0.0730.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021084
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_it1.7753.5012006
X-RAY DIFFRACTIONr_mcbond_other1.7713.4992005
X-RAY DIFFRACTIONr_mcangle_it2.8555.2362553
X-RAY DIFFRACTIONr_mcangle_other2.8565.2382554
X-RAY DIFFRACTIONr_scbond_it1.8743.5823140
X-RAY DIFFRACTIONr_scbond_other1.8683.5813139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1185.2684606
X-RAY DIFFRACTIONr_long_range_B_refined5.56238.2836232
X-RAY DIFFRACTIONr_long_range_B_other5.36837.7716099
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 134 -
Rwork0.312 2511 -
obs--95.94 %

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