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- PDB-5j8n: Exonuclease III homologue Mm3148 from Methanosarcina mazei -

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Basic information

Entry
Database: PDB / ID: 5j8n
TitleExonuclease III homologue Mm3148 from Methanosarcina mazei
ComponentsExodeoxyribonuclease III
KeywordsHYDROLASE / exonuclease III homologue / endonuclease / magnesium binding
Function / homology
Function and homology information


: / exodeoxyribonuclease III / endonuclease activity / DNA repair / 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
Exodeoxyribonuclease III
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsLakomek, K. / Dickmanns, A. / Ficner, R.
CitationJournal: To Be Published
Title: Structure of the archael ExoIII homologue Mm3148 at 1.4 Angstrom
Authors: Lakomek, K. / Dickmanns, A. / Ber, S. / Fritz, H.-J. / Ficner, R.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 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

Downloads & links

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Assembly

Deposited unit
A: Exodeoxyribonuclease III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0363
Polymers29,8181
Non-polymers2192
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-1 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.726, 64.564, 84.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exodeoxyribonuclease III


Mass: 29817.801 Da / Num. of mol.: 1 / Mutation: P2A, A118M, M209Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea)
Strain: ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88
Gene: MM_3148 / Plasmid: pET21-d derivative / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL / References: UniProt: Q8PSD1, exodeoxyribonuclease III
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.15 Å3/Da / Density % sol: 42.72 % / Description: plate-like shape
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20 % (w/v) PEG 8000, 20 % (w/v) PEG 400, 100 mM Tris/HCl pH 8.5, 100 mM MgCl2 mixed 1:1 with 10 mg/ml protein dissolved in 300 mM NaCl, 10 mM KHEPES pH 7.6, 2 mM DTT and addition of a seed ...Details: 20 % (w/v) PEG 8000, 20 % (w/v) PEG 400, 100 mM Tris/HCl pH 8.5, 100 mM MgCl2 mixed 1:1 with 10 mg/ml protein dissolved in 300 mM NaCl, 10 mM KHEPES pH 7.6, 2 mM DTT and addition of a seed stock solution (1/10 volume)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 16, 2007
RadiationMonochromator: 0.99 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.44→15 Å / Num. obs: 47242 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 14.63 Å2 / Rmerge(I) obs: 0.052 / Net I/av σ(I): 32.105 / Net I/σ(I): 13.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.44-1.496.30.2741100
1.49-1.556.30.2091100
1.55-1.626.30.1621100
1.62-1.716.30.1281100
1.71-1.816.30.11100
1.81-1.956.30.0751100
1.95-2.156.30.061100
2.15-2.466.30.0521100
2.46-3.096.20.0461100
3.09-155.90.041199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FZI

3fzi


Resolution: 1.44→14.831 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1713 2398 5.09 %
Rwork0.1468 --
obs0.148 47150 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.67 Å2 / Biso mean: 21.2763 Å2 / Biso min: 9.48 Å2
Refinement stepCycle: final / Resolution: 1.44→14.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 14 317 2433
Biso mean--42.24 30.71 -
Num. residues----258
Refinement TLS params.Method: refined / Origin x: -17.8847 Å / Origin y: -2.734 Å / Origin z: 3.3491 Å
111213212223313233
T0.0825 Å20.0047 Å2-0.0004 Å2-0.0823 Å2-0.01 Å2--0.0944 Å2
L0.927 °2-0.0312 °2-0.0272 °2-1.3692 °2-0.2012 °2--0.8146 °2
S-0.0174 Å °-0.038 Å °0.0677 Å °0.0126 Å °0.0073 Å °-0.0671 Å °-0.0251 Å °-0.0068 Å °0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 259
2X-RAY DIFFRACTION1allC1
3X-RAY DIFFRACTION1allW1 - 263
4X-RAY DIFFRACTION1allW264 - 317
5X-RAY DIFFRACTION1allF1

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