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- PDB-3w2x: Crystal structure of DNA uridine endonuclease Mth212 -

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Basic information

Entry
Database: PDB / ID: 3w2x
TitleCrystal structure of DNA uridine endonuclease Mth212
ComponentsExodeoxyribonuclease
KeywordsHYDROLASE / alpha/beta-sandwich / DNA binding
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
FORMIC ACID / DNA uridine endonuclease
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTabata, N. / Shida, T. / Arai, R.
CitationJournal: To be Published
Title: Crystal structure of DNA uridine endonuclease Mth212
Authors: Tabata, N. / Shida, T. / Arai, R.
History
DepositionDec 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_dist_value / _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_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_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)30,8345
Polymers30,6721
Non-polymers1624
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.481, 61.481, 132.716
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


Mass: 30671.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H
Gene: MTH212, MTH_212 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.36 Å3/Da / Density % sol: 47.9 % / Mosaicity: 0.621 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG3350, 50mM Magnesium formate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 19, 2011
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36324 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.073 / Χ2: 1.006 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.6-1.66110.5984.837520.918100
1.66-1.7211.20.4376.837230.949100
1.72-1.811.20.3578.737370.995100
1.8-1.910.70.3578.137251.141100
1.9-2.0211.10.17113.537281.068100
2.02-2.1711.30.09825.237431100
2.17-2.3910.20.09218.436091.02296.4
2.39-2.7411.30.05737.337280.971100
2.74-3.45110.05135.937520.98799.9
3.45-507.70.04923.228271.02774.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZI

3fzi


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.707 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 1778 5 %RANDOM
Rwork0.2131 ---
obs0.2144 35667 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.72 Å2 / Biso mean: 29.457 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20.41 Å20 Å2
2--0.83 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 10 187 2334
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222211
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.9412978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.455257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8222.81121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82115383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2751523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211730
X-RAY DIFFRACTIONr_mcbond_it0.5051.51278
X-RAY DIFFRACTIONr_mcangle_it0.87822063
X-RAY DIFFRACTIONr_scbond_it1.4413933
X-RAY DIFFRACTIONr_scangle_it2.1774.5915
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 145 -
Rwork0.23 2629 -
all-2774 -
obs-2774 99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7535-0.42870.10431.77830.06732.51230.0787-0.0582-0.1547-0.1494-0.04320.24940.0884-0.107-0.03550.1257-0.0236-0.04290.0982-0.00290.1561-40.234.56718.3468
21.2887-1.0021-0.8112.42360.32463.21220.0521-0.0203-0.1985-0.1901-0.02630.28220.0928-0.1611-0.02580.1392-0.0108-0.04520.1277-0.0090.1714-39.85668.315217.1073
39.1012-1.3765-1.54433.4251-0.63038.40150.36141.1374-0.6027-0.9931-0.18920.5270.2449-0.8216-0.17220.36050.0537-0.21170.2109-0.08930.1688-44.17158.42995.2263
43.2957-0.8375-0.6992.49250.20073.11170.08730.194-0.0908-0.3974-0.10240.05530.13420.03670.01510.21930.0081-0.0280.1296-0.00680.1147-36.062512.40488.6273
50.8975-0.60110.51431.9494-0.63631.18710.03250.11030.1031-0.2125-0.1355-0.1788-0.02930.20510.10310.1382-0.0060.01440.1540.00820.1314-29.24117.008412.6681
65.35674.97774.37978.49670.79576.361-0.1616-0.2820.39580.3706-0.07710.4227-0.564-0.38140.23870.179-0.0091-0.02510.1195-0.03740.1329-35.50524.278322.6618
72.0713-0.95140.32532.5688-0.18232.28460.0220.2181-0.002-0.2254-0.1936-0.45620.10370.4940.17170.0618-0.02050.04230.21170.05770.1648-17.470910.677117.0965
81.4819-0.65360.22763.71890.19730.7907-0.0868-0.01280.2671-0.0055-0.0784-0.2635-0.23170.14810.16530.1564-0.0633-0.05040.1418-0.0010.1486-24.938320.482123.9294
92.69320.14930.04453.0036-0.67722.8836-0.0265-0.0217-0.19440.1373-0.1838-0.44140.2130.44790.21040.06710.0044-0.04810.20040.03920.1678-17.2567-1.680431.4457
100.9071-1.165-0.35876.85290.37782.51710.0231-0.11780.06490.1933-0.3055-0.5872-0.24040.42670.28250.0416-0.0749-0.07260.20990.06140.2087-15.885611.197928.5515
110.587-0.26060.22632.7289-0.38390.9506-0.0577-0.0246-0.01030.09180.0324-0.0660.02290.05950.02530.1425-0.019-0.01840.1656-0.00480.1335-28.1082.273629.9968
121.0437-0.39870.78493.90660.49122.4256-0.0567-0.2138-0.02710.21180.10440.2477-0.0007-0.1068-0.04780.1034-0.0239-0.00990.15190.0030.1324-35.67337.964729.3238
1315.9492-3.154-1.475723.86082.8896.5256-0.1836-0.4750.9826-0.1327-0.0839-0.0972-0.603-1.65720.26760.16240.1632-0.01030.4804-0.12480.107-40.698920.207632.9463
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 43
3X-RAY DIFFRACTION3A44 - 53
4X-RAY DIFFRACTION4A54 - 67
5X-RAY DIFFRACTION5A68 - 101
6X-RAY DIFFRACTION6A102 - 107
7X-RAY DIFFRACTION7A108 - 135
8X-RAY DIFFRACTION8A136 - 154
9X-RAY DIFFRACTION9A155 - 170
10X-RAY DIFFRACTION10A171 - 189
11X-RAY DIFFRACTION11A190 - 229
12X-RAY DIFFRACTION12A230 - 253
13X-RAY DIFFRACTION13A254 - 257

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