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- PDB-3b0x: K263A mutant of PolX from Thermus thermophilus HB8 complexed with... -

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Basic information

Entry
Database: PDB / ID: 3b0x
TitleK263A mutant of PolX from Thermus thermophilus HB8 complexed with Ca-dGTP
ComponentsDNA polymerase beta family (X family)
KeywordsTRANSFERASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / POLXc / PHP / DNA polymerase / dRP lyase / 3'-5' exonuclease / AP endonuclease / DNA repair / nucleotide / DNA
Function / homology
Function and homology information


phosphoric ester hydrolase activity / DNA-(apurinic or apyrimidinic site) lyase / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA binding / zinc ion binding / cytosol
Similarity search - Function
DNA polymerase/3'-5' exonuclease PolX-like / : / : / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / RuvA domain 2-like / Helix-hairpin-helix domain ...DNA polymerase/3'-5' exonuclease PolX-like / : / : / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / RuvA domain 2-like / Helix-hairpin-helix domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase family X, beta-like / DNA polymerase beta, N-terminal domain-like / Metal-dependent hydrolases / 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 beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA polymerase beta
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsNakane, S. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The structural basis of the kinetic mechanism of a gap-filling X-family DNA polymerase that binds Mg(2+)-dNTP before binding to DNA.
Authors: Nakane, S. / Ishikawa, H. / Nakagawa, N. / Kuramitsu, S. / Masui, R.
History
DepositionJun 17, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Structure summary
Revision 1.2Nov 1, 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.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_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: DNA polymerase beta family (X family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9809
Polymers64,1461
Non-polymers8348
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.088, 53.202, 84.859
Angle α, β, γ (deg.)90.000, 107.650, 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 DNA polymerase beta family (X family)


Mass: 64146.379 Da / Num. of mol.: 1 / Mutation: K263A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: PolX, TTHA1150 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2/pLysS / References: UniProt: Q5SJ64, DNA-directed DNA polymerase

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Non-polymers , 5 types, 559 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M potassium chloride, 0.01M calcium chloride, 0.005M sodium cacodylate (pH 6.0), 10% polyethylene glycol 4000 (v/v), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2011
Diffraction measurementDetails: 0.50 degrees, 4.7 sec, detector distance 120.00 mm / Method: \w scans
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionAv R equivalents: 0.044 / Number: 466387
ReflectionResolution: 1.36→50 Å / Num. obs: 125330 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 26.642
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.009 / Rsym value: 0.258 / % possible all: 99.6
Cell measurementReflection used: 466387

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.57 Å17.32 Å
Translation1.57 Å17.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.5.0110refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AU2

3au2


Resolution: 1.36→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.445 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 6281 5 %RANDOM
Rwork0.171 ---
obs0.1724 125120 99.43 %-
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: 58.16 Å2 / Biso mean: 20.4946 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.15 Å2
2--0.49 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.36→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 38 551 5108
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224662
X-RAY DIFFRACTIONr_angle_refined_deg1.3826319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83222.85214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76315820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5291551
X-RAY DIFFRACTIONr_chiral_restr0.0830.2691
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213543
X-RAY DIFFRACTIONr_mcbond_it1.1791.52868
X-RAY DIFFRACTIONr_mcangle_it1.87624587
X-RAY DIFFRACTIONr_scbond_it2.59331794
X-RAY DIFFRACTIONr_scangle_it3.9464.51728
X-RAY DIFFRACTIONr_rigid_bond_restr1.3334662
X-RAY DIFFRACTIONr_sphericity_free5.9633558
X-RAY DIFFRACTIONr_sphericity_bonded3.76734567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.361-1.3960.194570.1668720924399.286
1.396-1.4350.1774250.1488630906899.857
1.435-1.4760.1674660.1338289876999.84
1.476-1.5220.1724260.1338066850199.894
1.522-1.5710.1674240.1267825826599.806
1.571-1.6260.164200.1257558799499.8
1.626-1.6880.163830.137330772699.832
1.688-1.7570.1643730.1347051743299.892
1.757-1.8350.1753650.1446774714999.86
1.835-1.9240.1893520.1526471683399.854
1.924-2.0280.1813120.1616146646599.892
2.028-2.1510.1932960.1655844614799.886
2.151-2.2990.1962950.1655509581299.862
2.299-2.4830.2232740.1785122540199.907
2.483-2.7190.2092560.1914696496199.819
2.719-3.0390.2332140.2034287450899.845
3.039-3.5070.2221960.2043791399299.875
3.507-4.290.2081600.1843164338698.169
4.29-6.0440.2371280.2052436265696.536
6.044-500.201590.2311130153277.611

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