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- PDB-3fzi: 1.9 Angstrom structure of the thermophilic exonuclease III homolo... -

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Basic information

Entry
Database: PDB / ID: 3fzi
Title1.9 Angstrom structure of the thermophilic exonuclease III homologue Mth0212
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / alpha/beta-sandwich / double-strand specific 3'-5' exonuclease / AP endonuclease / 2'-deoxyuridine endonuclease
Function / homology
Function and homology information


double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / phosphoric diester hydrolase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / base-excision repair / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
AP endonuclease 1, binding site / AP endonucleases family 1 signature 1. / AP endonuclease 1 / AP endonucleases family 1 profile. / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsLakomek, K. / Dickmanns, A. / Ficner, R.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA
Authors: Lakomek, K. / Dickmanns, A. / Ciirdaeva, E. / Schomacher, L. / Ficner, R.
#1: Journal: Nucleic Acids Res. / Year: 2006
Title: The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease
Authors: Georg, J. / Schomacher, L. / Chong, J.P.J. / Majernik, A.I. / Raabe, M. / Urlaub, H. / Muller, S. / Ciirdaeva, E. / Kramer, W. / Fritz, H.-J.
History
DepositionJan 26, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4552
Polymers31,4311
Non-polymers241
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.040, 56.040, 161.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Exodeoxyribonuclease / Mth0212


Mass: 31430.650 Da / Num. of mol.: 1 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Details: lacking the gene "ung"
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (WT) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21_UX / References: UniProt: O26314, exodeoxyribonuclease III
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir: 20 % PEG 1500, 100mM HEPES pH 7.5; protein solution: 600mM NaCl, 20mM HEPES-KOH pH 7.6, 2mM DTT, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8015 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8015 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22592 / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.058 / Χ2: 1.044 / Net I/σ(I): 36.32
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.977.30.55822181.18100
1.97-2.057.50.38822760.982100
2.05-2.147.50.29122660.992100
2.14-2.257.50.22322591.164100
2.25-2.397.50.16822401.021100
2.39-2.587.60.11122631.04100
2.58-2.847.60.07622591.04100
2.84-3.257.60.04322581.02299.9
3.25-4.097.60.02822681.0199.9
4.09-507.40.02322850.99798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DE9

1de9


Resolution: 1.9→48.51 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.248 / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.772 / SU B: 4.696 / SU ML: 0.137 / SU R Cruickshank DPI: 0.176 / SU Rfree: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26161 1151 5.1 %RANDOM
Rwork0.19755 21351 --
obs0.20081 22502 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.79 Å2 / Biso mean: 28.644 Å2 / Biso min: 13.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å20.72 Å20 Å2
2--1.45 Å20 Å2
3----2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 1 292 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222210
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9422980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16322.81121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49215384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4571523
X-RAY DIFFRACTIONr_chiral_restr0.110.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021730
X-RAY DIFFRACTIONr_nbd_refined0.2150.21281
X-RAY DIFFRACTIONr_nbtor_refined0.3210.21521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2311
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.219
X-RAY DIFFRACTIONr_mcbond_it0.9931.51309
X-RAY DIFFRACTIONr_mcangle_it1.64922066
X-RAY DIFFRACTIONr_scbond_it2.22831032
X-RAY DIFFRACTIONr_scangle_it3.2264.5914
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 68 -
Rwork0.282 1576 -
all-1644 -
obs--99.4 %

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