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- PDB-6ghs: Modification dependent TagI restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 6ghs
TitleModification dependent TagI restriction endonuclease
ComponentsTagI restriction endonuclease
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / TYPE II / TYPE IV / CYTOSINE MODIFICATION / 5-METHYLCYTOSINE / 5MC / 5-HYDROXYMETHYLCYTOSINE / 5HMC / SRA / HNH / BBA-ME NUCLEASE / ScoA3IV / SCO5333 / TbiR51I / TBIS1
Function / homology
Function and homology information


ubiquitin protein ligase activity / protein ubiquitination / metal ion binding
Similarity search - Function
HNH endonuclease / UHRF1/2-like / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / HNH nuclease / PUA-like superfamily
Similarity search - Domain/homology
TagI restriction endonuclease
Similarity search - Component
Biological speciesThermocrispum agreste (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsKisiala, M. / Copelas, A. / Czapinska, H. / Xu, S. / Bochtler, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Crystal structure of the modification-dependent SRA-HNH endonuclease TagI.
Authors: Kisiala, M. / Copelas, A. / Czapinska, H. / Xu, S.Y. / Bochtler, M.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TagI restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0863
Polymers33,9971
Non-polymers882
Water95553
1
A: TagI restriction endonuclease
hetero molecules

A: TagI restriction endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1716
Polymers67,9942
Non-polymers1774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3430 Å2
ΔGint-29 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.963, 72.963, 207.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein TagI restriction endonuclease


Mass: 33997.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocrispum agreste (bacteria) / Plasmid: pTXB1 / Production host: Escherichia coli B (bacteria) / Strain (production host): C2566 / References: UniProt: A0A3F2YM30*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 4.4 Å3/Da / Density % sol: 72.07 %
Crystal growTemperature: 294 K / Method: liquid diffusion / pH: 7.5
Details: A5 Morpheus Buffer (10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M MgCl2, 0.03 M CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5)
PH range: 7.5

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 16, 2018 / Details: HELIOS multilayer optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.92→20 Å / Num. obs: 12496 / % possible obs: 96.1 % / Redundancy: 3.23 % / Rmerge(I) obs: 0.2386 / Rsym value: 0.2196 / Net I/σ(I): 4.38
Reflection shellResolution: 2.92→3.02 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6983 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.9485 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
SAINTdata reduction
SADABSdata reduction
SAINTdata scaling
SADABSdata scaling
PHASERphasing
FFFEARphasing
BALBESphasing
BUCCANEERmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3clz, 5mkw

3clz

5mkw


Resolution: 2.92→20 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.582 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.523 / ESU R Free: 0.293
Details: THE IDENTITY OF THE METAL ION IN THE ACTIVE SITE (LIGATED BY HIS 254 AND ASP 258) IS UNCERTAIN. UNDER PHYSIOLOGICAL CONDITIONS THIS SITE IS MOST LIKELY OCCUPIED BY A MG2+ ION. HOWEVER, SINCE ...Details: THE IDENTITY OF THE METAL ION IN THE ACTIVE SITE (LIGATED BY HIS 254 AND ASP 258) IS UNCERTAIN. UNDER PHYSIOLOGICAL CONDITIONS THIS SITE IS MOST LIKELY OCCUPIED BY A MG2+ ION. HOWEVER, SINCE THE CONCENTRATION OF EDTA IN THE PROTEIN BUFFER EXCEEDS THE MG2+ CONCENTRATION IN THE RESERVOIR BUFFER ALMOST 20 TIMES WE PREDICT THAT THE MG2+ IONS (AND CA2+ IONS THAT WERE ALSO PRESENT IN THE BUFFER) WERE DEPLETED. UNFORTUNATELY, THE RESOLUTION OF THE DIFFRACTION DATA IS NOT HIGH ENOUGH TO PERFORM THE ANALYSIS OF THE METAL-LIGAND DISTANCES, BUT SINCE SODIUM IONS WERE ABUNDANT IN BOTH BUFFERS AND SINCE THE ELECTRON DENSITY LEVEL OF THE ION ROUGHLY CORRESPONDS TO ONE OF THE SURROUNDING PROTEIN AND SOLVENT ATOMS, WE HAVE TENTATIVELY ASSIGNED THE METAL IN THE ACTIVE SITE AS A NA+ ION. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22309 607 4.9 %RANDOM
Rwork0.19242 ---
obs0.19389 11890 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 51.062 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å2-0 Å20 Å2
2--1.54 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.92→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 2 53 2267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192278
X-RAY DIFFRACTIONr_bond_other_d0.0010.022060
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9433092
X-RAY DIFFRACTIONr_angle_other_deg0.93234777
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39323.391115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90615358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0541520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212608
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
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_it2.6895.0481143
X-RAY DIFFRACTIONr_mcbond_other2.6845.0471142
X-RAY DIFFRACTIONr_mcangle_it4.6237.5521427
X-RAY DIFFRACTIONr_mcangle_other4.6227.5541428
X-RAY DIFFRACTIONr_scbond_it2.6745.3431135
X-RAY DIFFRACTIONr_scbond_other2.6755.3421134
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7417.8861665
X-RAY DIFFRACTIONr_long_range_B_refined7.48656.8282365
X-RAY DIFFRACTIONr_long_range_B_other7.48156.8452362
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.917→2.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 43 -
Rwork0.363 807 -
obs--93.51 %

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