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- PDB-2ihm: Polymerase mu in ternary complex with gapped 11mer DNA duplex and... -

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Basic information

Entry
Database: PDB / ID: 2ihm
TitlePolymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide
Components
  • 5'-D(*CP*AP*GP*TP*AP*T)-3'
  • 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
  • 5'-D(P*GP*CP*CP*G)-3'
  • DNA polymerase mu
KeywordsTransferase/DNA / polymerase / helix-turn-helix / Transferase-DNA COMPLEX
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / somatic hypermutation of immunoglobulin genes / B cell differentiation / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMoon, A.F. / Pedersen, L.C. / Kunkel, T.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2007
Title: Structural insight into the substrate specificity of DNA Polymerase mu.
Authors: Moon, A.F. / Garcia-Diaz, M. / Bebenek, K. / Davis, B.J. / Zhong, X. / Ramsden, D.A. / Kunkel, T.A. / Pedersen, L.C.
History
DepositionSep 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
P: 5'-D(*CP*AP*GP*TP*AP*T)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
U: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
Q: 5'-D(*CP*AP*GP*TP*AP*T)-3'
E: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase mu
B: DNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,99115
Polymers93,9418
Non-polymers1,0507
Water3,297183
1
T: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
P: 5'-D(*CP*AP*GP*TP*AP*T)-3'
D: 5'-D(P*GP*CP*CP*G)-3'
A: DNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9739
Polymers46,9704
Non-polymers1,0035
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
U: 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'
Q: 5'-D(*CP*AP*GP*TP*AP*T)-3'
E: 5'-D(P*GP*CP*CP*G)-3'
B: DNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0186
Polymers46,9704
Non-polymers472
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.028, 96.085, 73.090
Angle α, β, γ (deg.)90.00, 106.55, 90.00
Int Tables number4
Space group name H-MP1211
DetailsEach asymmetric unit contains two monomers of polymerase mu. However, the monomeric form of polymerase mu is the biological unit.

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Components

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DNA chain , 3 types, 6 molecules TUPQDE

#1: DNA chain 5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'


Mass: 3358.211 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*AP*GP*TP*AP*T)-3'


Mass: 1808.229 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*GP*CP*CP*G)-3'


Mass: 1191.818 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Protein , 1 types, 2 molecules AB

#4: Protein DNA polymerase mu / / Pol Mu


Mass: 40612.043 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Polm / Plasmid: pGEX4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) - RIL / References: UniProt: Q9JIW4, DNA-directed DNA polymerase

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Non-polymers , 4 types, 190 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-D3T / 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE


Type: DNA OH 3 prime terminus / Mass: 466.169 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N2O13P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.53 Å3/Da / Density % sol: 51.37 %
Crystal growDetails: 0.095M Na Citrate pH 5.6, 19% ispropanol, 19% PEG4000, and 5% glycerol
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES11
2ispropanol11
3PEG400011
4glycerol11
5H2O11
6HEPES12
7ispropanol12
8PEG400012
9glycerol12

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 21, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 36847 / Num. obs: 36737 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 16.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3645 / Rsym value: 0.505 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
MAR345345DTBdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: murine TdT - 1JMS

1jms


Resolution: 2.4→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1653 -random
Rwork0.23 ---
all0.232 35276 --
obs0.232 35276 99.7 %-
Displacement parametersBiso mean: 58.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å23.39 Å2
2--5.79 Å20 Å2
3----6.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 850 61 183 6340
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_improper_angle_d1.17
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.408 229 -
Rwork0.379 --
obs-5039 86.1 %

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