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- PDB-2hpm: Eubacterial and Eukaryotic Replicative DNA Polymerases are not Ho... -

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Basic information

Entry
Database: PDB / ID: 2hpm
TitleEubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III
ComponentsDNA Polymerase III alpha subunit
KeywordsTRANSFERASE / Nucleotidyltransferase fold
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA replication / nucleic acid binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain ...Bacterial DNA polymerase III alpha subunit, thumb domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Metal-dependent hydrolases / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TRIPHOSPHATE / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.7 Å
AuthorsBailey, S. / Wing, R.A. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: The Structure of T. aquaticus DNA Polymerase III Is Distinct from Eukaryotic Replicative DNA Polymerases.
Authors: Bailey, S. / Wing, R.A. / Steitz, T.A.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _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 III alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0888
Polymers137,5791
Non-polymers5087
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: DNA Polymerase III alpha subunit
hetero molecules

A: DNA Polymerase III alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)276,17516
Polymers275,1592
Non-polymers1,01714
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area6420 Å2
ΔGint-268 kcal/mol
Surface area103430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.442, 185.724, 125.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA Polymerase III alpha subunit


Mass: 137579.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9XDH5, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-3PO / TRIPHOSPHATE / Polyphosphate


Mass: 257.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H5O10P3

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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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 550 MME 0.2M NaCl 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.7→20 Å / Num. obs: 20864 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 3.7→3.83 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.7→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.883 / SU B: 103.532 / SU ML: 0.684 / Cross valid method: THROUGHOUT / ESU R Free: 0.775
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.31086 1115 5.1 %RANDOM
Rwork0.23952 ---
obs0.24303 20864 99.94 %-
all-21979 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 131.235 Å2
Baniso -1Baniso -2Baniso -3
1-5.94 Å20 Å20 Å2
2---0.18 Å20 Å2
3----5.76 Å2
Refinement stepCycle: LAST / Resolution: 3.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9127 0 19 0 9146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229319
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.98612582
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84651133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84622.967455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.55151647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471598
X-RAY DIFFRACTIONr_chiral_restr0.0920.21371
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027095
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.24414
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26093
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2339
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2610.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5835831
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.47249096
X-RAY DIFFRACTIONr_scbond_it6.5163894
X-RAY DIFFRACTIONr_scangle_it10.41993486
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.7→3.794 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 91 -
Rwork0.309 1462 -
obs--99.74 %
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)
13.85241.12271.41447.7361-0.39424.0967-0.1475-0.65150.33920.59160.1505-0.2478-0.20210.0557-0.003-0.4890.17220.0488-0.6314-0.1311-0.6491-43.952116.164521.7345
25.54859.30816.965818.576616.961718.14451.1889-0.29940.41622.2602-0.49521.78570.8898-3.1875-0.6937-0.12340.06840.0882-0.0490.11860.4186-63.8108-14.669818.8927
30.55962.371-0.772610.37-2.81541.71450.0549-0.1251-0.27320.4615-0.0132-0.0531-0.2692-0.2887-0.0417-0.5635-0.04510.0248-0.52370.0974-0.5434-50.5336-21.149416.0299
410.90774.04883.585413.76320.822811.46590.1006-0.0838-0.1838-0.3085-0.26381.40950.6426-1.9330.1632-0.7322-0.36160.0027-0.2880.2591-0.1463-67.7423-39.478819.2313
513.89273.81313.75635.59023.55217.7683-0.2041-0.6592-0.64880.50240.3469-1.39680.53470.5401-0.14280.18260.3054-0.3185-0.20080.12070.2136-22.965-2.77734.3474
66.9327-0.1914-2.02637.67610.220517.36190.1327-0.1188-0.9037-0.2549-0.1019-0.47670.30790.2413-0.0308-0.8847-0.20190.0453-0.80790.0838-0.5241-34.3468-40.86818.5545
711.6456-3.6607-4.46337.10154.284214.6859-0.4929-1.93680.15931.56760.46640.1037-0.67780.32830.0265-0.2448-0.29410.061-0.42990.3325-0.351-47.5337-37.013745.1214
83.31830.7538-0.27685.4443-1.641911.8818-0.15750.5989-0.1537-0.6518-0.0654-0.6722-0.2911.24920.2229-0.5775-0.08150.2239-0.2332-0.0678-0.2948-16.69-32.1615-11.666
919.6615-1.4006-1.136311.4209-0.689614.4312-0.0408-0.06950.8008-0.1125-0.1235-0.5662-0.7233-0.03860.1643-0.5695-0.0517-0.336-0.10220.11840.0092-1.8994-22.950116.4848
1014.8905-6.67345.220213.2853-4.00322.90650.16430.64150.2998-0.0175-0.62590.47031.22540.29780.4616-0.23170.1457-0.17890.33410.02150.102511.8059-40.684723.8252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 2855 - 285
2X-RAY DIFFRACTION2AA286 - 305286 - 305
3X-RAY DIFFRACTION3AA400 - 492400 - 492
4X-RAY DIFFRACTION3AA575 - 622575 - 622
5X-RAY DIFFRACTION4AA306 - 399306 - 399
6X-RAY DIFFRACTION5AA493 - 574493 - 574
7X-RAY DIFFRACTION6AA623 - 699623 - 699
8X-RAY DIFFRACTION6AA814 - 835814 - 835
9X-RAY DIFFRACTION7AA700 - 813700 - 813
10X-RAY DIFFRACTION8AA836 - 1013836 - 1013
11X-RAY DIFFRACTION9AA1014 - 11281014 - 1128
12X-RAY DIFFRACTION10AA1129 - 12051129 - 1205

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