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- PDB-5dmu: Structure of the NHEJ polymerase from Methanocella paludicola -

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Basic information

Entry
Database: PDB / ID: 5dmu
TitleStructure of the NHEJ polymerase from Methanocella paludicola
ComponentsNHEJ Polymerase
KeywordsTRANSFERASE / Archaeal Proteins / Biocatalysis / DNA Repair Enzymes / DNA-Directed DNA Polymerase / Protein Structure / Ribonucleotides
Function / homologyDNA ligase D, polymerase domain / : / LigD, primase-polymerase domain / ligase activity / DNA recombination / DNA repair / ATP binding / metal ion binding / DNA ligase D polymerase domain-containing protein
Function and homology information
Biological speciesMethanocella paludicola (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.949 Å
AuthorsBrissett, N.C. / Bartlett, E.J. / Doherty, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council(BB/J018643/1) United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular basis for DNA strand displacement by NHEJ repair polymerases.
Authors: Bartlett, E.J. / Brissett, N.C. / Plocinski, P. / Carlberg, T. / Doherty, A.J.
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NHEJ Polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5827
Polymers34,1511
Non-polymers4316
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-22 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.420, 60.550, 59.410
Angle α, β, γ (deg.)90.000, 101.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NHEJ Polymerase


Mass: 34150.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocella paludicola (strain DSM 17711 / JCM 13418 / NBRC 101707 / SANAE) (archaea)
Strain: DSM 17711 / JCM 13418 / NBRC 101707 / SANAE / Gene: MCP_2125 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D1Z0H5

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Non-polymers , 5 types, 294 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 200 mM ammonium sulfate, 20% (w/v) PEG 335

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 12, 2013 / Details: VariMax-HF mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.949→58.315 Å / Num. all: 22140 / Num. obs: 22140 / % possible obs: 97.4 % / Redundancy: 3.5 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.084 / Rsym value: 0.071 / Net I/av σ(I): 9.94 / Net I/σ(I): 13.8 / Num. measured all: 77013
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.95-2.052.60.23.8730727680.140.24.984
2.05-2.183.50.1654.61091931180.1030.1657.2100
2.18-2.333.60.12861054529540.0790.1289.3100
2.33-2.523.60.1087.1987727360.0660.10811.1100
2.52-2.763.60.0888.6911525110.0540.08813.2100
2.76-3.083.70.06711.2833122790.0410.06716.2100
3.08-3.563.70.04814.8741720320.0290.04821.3100
3.56-4.363.70.03816.2627617140.0230.03826.6100
4.36-6.163.60.03717.2483613410.0230.03725.9100
6.16-13.933.50.03418.423906870.0220.03425.191.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å13.93 Å
Translation2 Å13.93 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
CrystalCleardata collection
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IRU

2iru


Resolution: 1.949→58.31 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.1799 / WRfactor Rwork: 0.1376 / FOM work R set: 0.8787 / SU B: 3.175 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1546 / SU Rfree: 0.1413 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 1131 5.1 %RANDOM
Rwork0.1478 ---
obs0.1502 20996 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 59.76 Å2 / Biso mean: 15.014 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.13 Å2
2--0.02 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 1.949→58.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 25 288 2717
Biso mean--28.59 26.29 -
Num. residues----301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192507
X-RAY DIFFRACTIONr_angle_refined_deg1.821.973391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89722.479121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44215426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8971527
X-RAY DIFFRACTIONr_chiral_restr0.1350.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211932
X-RAY DIFFRACTIONr_mcbond_it1.0941.1871218
X-RAY DIFFRACTIONr_mcangle_it1.7011.7681526
X-RAY DIFFRACTIONr_scbond_it2.3591.4791289
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 62 -
Rwork0.168 1175 -
all-1237 -
obs--74.56 %

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