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- PDB-6ak5: Binary Complex of Human DNA Polymerase Mu with MnGTP -

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Basic information

Entry
Database: PDB / ID: 6ak5
TitleBinary Complex of Human DNA Polymerase Mu with MnGTP
ComponentsDNA-directed DNA/RNA polymerase mu
KeywordsTRANSFERASE / DNA Polymerase Mu / DNA break repair / Transferase-rNTP complex
Function / homology
Function and homology information


somatic hypermutation of immunoglobulin genes / B cell differentiation / base-excision repair / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
DNA polymerase beta, palm domain / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase lambda, fingers domain / DNA polymerase beta-like, N-terminal domain / DNA-directed DNA polymerase X / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCT domain / DNA polymerase beta, thumb domain / DNA-directed DNA/RNA polymerase mu ...DNA polymerase beta, palm domain / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase lambda, fingers domain / DNA polymerase beta-like, N-terminal domain / DNA-directed DNA polymerase X / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCT domain / DNA polymerase beta, thumb domain / DNA-directed DNA/RNA polymerase mu / BRCT domain superfamily / DNA polymerase, thumb domain superfamily / Fingers domain of DNA polymerase lambda / Helix-hairpin-helix domain / DNA polymerase beta thumb / DNA polymerase beta palm / DNA polymerase family X / DNA polymerase, thumb domain / Beta Polymerase; domain 3 / DNA polymerase beta, N-terminal domain-like / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
DNA-directed DNA/RNA polymerase mu
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsChang, Y.K. / Wu, W.J. / Tsai, M.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Human DNA Polymerase mu Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions.
Authors: Chang, Y.K. / Huang, Y.P. / Liu, X.X. / Ko, T.P. / Bessho, Y. / Kawano, Y. / Maestre-Reyna, M. / Wu, W.J. / Tsai, M.D.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,36011
Polymers40,0541
Non-polymers1,30510
Water6,233346
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-87 kcal/mol
Surface area15850 Å2
Unit cell
γ
α
β
Length a, b, c (Å)124.918, 124.918, 50.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-746-

HOH

21A-903-

HOH

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Components

#1: Protein/peptide DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 40054.434 Da / Num. of mol.: 1 / Details: deletions 398-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Manganese
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 1.5 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 44337 / % possible obs: 99.5 % / Redundancy: 13.9 % / Rpim(I) all: 0.017 / Net I/σ(I): 45.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4360 / Rpim(I) all: 0.243 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.63 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24764 2167 4.9 %RANDOM
Rwork0.20838 ---
Obs0.21035 41690 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.7→88.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 69 346 3003
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0090.0192856
r_bond_other_d0.0020.022617
r_angle_refined_deg1.4281.9753907
r_angle_other_deg0.92136010
r_dihedral_angle_1_deg5.2745361
r_dihedral_angle_2_deg35.47323.233133
r_dihedral_angle_3_deg12.0415457
r_dihedral_angle_4_deg19.6591524
r_chiral_restr0.080.2422
r_gen_planes_refined0.0060.0213307
r_gen_planes_other0.0020.02701
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.6211.0271402
r_mcbond_other0.6211.0271401
r_mcangle_it1.1321.531774
r_mcangle_other1.1321.531775
r_scbond_it0.6341.2191454
r_scbond_other0.5751.1171414
r_scangle_it
r_scangle_other1.0281.6612071
r_long_range_B_refined5.10913.5793295
r_long_range_B_other4.73612.7913188
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 1.699→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 136 -
Rwork0.256 2758 -
Obs--89.43 %
Refinement TLS params.Method: refined / Origin x: 126.9412 Å / Origin y: 89.2245 Å / Origin z: 50.7208 Å
111213212223313233
T0.0241 Å20.0159 Å20.0219 Å2-0.0686 Å20.0129 Å2--0.052 Å2
L0.3845 °20.0567 °20.0273 °2-0.4712 °2-0.1578 °2--0.2563 °2
S0.06 Å °-0.0081 Å °0.1341 Å °0.0112 Å °-0.0668 Å °-0.0152 Å °0.0381 Å °-0.0031 Å °0.0067 Å °
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Auth asym-ID: A

IDAuth seq-ID
1138 - 229
2230 - 290
3291 - 424
4425 - 494

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