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Open data
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Basic information
Entry | Database: PDB / ID: 3g2d | ||||||
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Title | Complex of Mth0212 and a 4 bp dsDNA with 3'-overhang | ||||||
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![]() | HYDROLASE/DNA / protein-DNA complex / dsDNA with 3'-overhang / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lakomek, K. / Dickmanns, A. / Ficner, R. | ||||||
![]() | ![]() 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 |
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Remark 285 | CRYST1 THE DEPOSITOR CONFIRM THE REPORTED SPACE GROUP P 1 21 1 DESPITE OF THE BETA ANGLE OF 90.0 ...CRYST1 THE DEPOSITOR CONFIRM THE REPORTED SPACE GROUP P 1 21 1 DESPITE OF THE BETA ANGLE OF 90.0 DEGREE. THE STRUCTURE COULD NOT BE REFINED IN A PRIMITIVE ORTHORHOMBIC SPACE GROUP - MOST LIKELY DUE TO SOME DISORDER IN THE CRYSTAL OR TWINNING. HOWEVER, THERE WAS NO INDICATION OF TWINNING. THE PRESENCE OF PEG MOLECULES IN ONLY ONE OF THE TWO PROTEIN MOLECULES IN THE ASYMMETRIC UNIT (ASU) AT EQUIVALENT POSITIONS (IN SPACE GROUP P21) AND DIFFERENCES IN THE DOUBLE-STRANDED DNA HELICES (DIFFERENT LENGTH OF ONE STRAND) BOUND BY THE TWO MOLECULES IN THE ASU E.G. ARGUED AGAINST MODEL BUILDING IN AN ORTHORHOMBIC SPACE GROUP. HOWEVER, THE USE OF A TWIN LAW MIGHT HAVE BEEN AN ADVANTAGE, BUT WAS NOT TAKEN INTO ACCOUNT DUE TO THE RESOLUTION OF 2.3A PREVENTING REFINEMENT WITH SHELXL AND DNA RESTRAINTS IN CNS LESS SUITABLE THAN THE RESTRAINTS USED BY REFMAC5 FOR EXAMPLE. THE STRUCTURE COULD BE REFINED TO REASONABLE R VALUES EVEN WITHOUT THE APPLICATION OF A TWIN LAW. THUS, THE REFINEMENT WAS CONTINUED IN THE SPACE GROUP P21. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.9 KB | Display | ![]() |
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PDB format | ![]() | 110 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3fziSC ![]() 3g00C ![]() 3g0aC ![]() 3g0rC ![]() 3g1kC ![]() 3g2cC ![]() 3g38C ![]() 3g3cC ![]() 3g3yC ![]() 3g4tC ![]() 3g8vC ![]() 3g91C ![]() 3ga6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 1
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31429.666 Da / Num. of mol.: 2 / Mutation: T2A, D151N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Delta H (DSM 1053) / Gene: mth0212, MTH212, MTH_212 / Plasmid: pET_B_001-mth212 (D151N) / Production host: ![]() ![]() |
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-DNA chain , 2 types, 4 molecules GHKI
#2: DNA chain | Mass: 2741.800 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 3021.964 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 4 types, 327 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-PG4 / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | THE 3'-OVERHANG OF THE DNA COMPRISES 4 AND 5 NUCLEOTIDES, RESPECTIVELY, ADJACENT TO THE TWO DOUBLE- ...THE 3'-OVERHANG OF THE DNA COMPRISES 4 AND 5 NUCLEOTIDE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 50mM MES pH 5.8, 10mM MgCl2 ; complex solution: 240mM NaCl, 8mM HEPES-KOH pH 7.6, 4mM DTT, 2mM MgCl2, 1mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, ...Details: reservoir: 5% (w/v) PEG 4000, 50mM KCl, 50mM MES pH 5.8, 10mM MgCl2 ; complex solution: 240mM NaCl, 8mM HEPES-KOH pH 7.6, 4mM DTT, 2mM MgCl2, 1mM KH2PO4/K2HPO4 pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.815 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 29120 / % possible obs: 93.8 % / Redundancy: 2.9 % / Rsym value: 0.055 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.191 / % possible all: 76.3 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3FZI Resolution: 2.3→48.55 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.862 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.787 / SU B: 7.971 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 107.75 Å2 / Biso mean: 28.354 Å2 / Biso min: 9.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→48.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2122 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.296→2.356 Å / Total num. of bins used: 20
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