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- PDB-4tr6: Crystal structure of DNA polymerase sliding clamp from Bacillus s... -

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Basic information

Entry
Database: PDB / ID: 4tr6
TitleCrystal structure of DNA polymerase sliding clamp from Bacillus subtilis
ComponentsDNA polymerase III subunit beta
KeywordsDNA BINDING PROTEIN / DNA polymerase / sliding clamp / processivity
Function / homology
Function and homology information


DNA polymerase III complex / nucleoid / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit / : / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBurnouf, D. / Olieric, V. / Ennifar, E. / Wolff, P.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Differential Modes of Peptide Binding onto Replicative Sliding Clamps from Various Bacterial Origins.
Authors: Wolff, P. / Amal, I. / Olieric, V. / Chaloin, O. / Gygli, G. / Ennifar, E. / Lorber, B. / Guichard, G. / Wagner, J. / Dejaegere, A. / Burnouf, D.Y.
History
DepositionJun 14, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2May 8, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
B: DNA polymerase III subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7703
Polymers84,7472
Non-polymers231
Water13,745763
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.220, 68.330, 85.310
Angle α, β, γ (deg.)65.77, 82.84, 86.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase III subunit beta


Mass: 42373.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: dnaN, dnaG, BSU00020 / Production host: Escherichia coli (E. coli) / References: UniProt: P05649, DNA-directed DNA polymerase
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 763 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M bis tris pH 6.5 and 28% PEG MME 2000 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00153 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 11, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00153 Å / Relative weight: 1
ReflectionResolution: 1.5→42.8 Å / Num. obs: 135911 / % possible obs: 95.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 24.22 Å2 / Net I/σ(I): 16.36

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→21.96 Å / Cor.coef. Fo:Fc: 0.9611 / Cor.coef. Fo:Fc free: 0.9524 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.065 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.068
RfactorNum. reflection% reflectionSelection details
Rfree0.2041 6815 5.02 %RANDOM
Rwork0.1761 ---
obs0.1775 135877 96.07 %-
Displacement parametersBiso mean: 32.03 Å2
Baniso -1Baniso -2Baniso -3
1--3.4179 Å24.0137 Å2-1.8942 Å2
2---1.2695 Å20.3945 Å2
3---4.6874 Å2
Refine analyzeLuzzati coordinate error obs: 0.204 Å
Refinement stepCycle: 1 / Resolution: 1.5→21.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11720 0 1 763 12484
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111829HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.221592HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2674SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes152HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1720HARMONIC5
X-RAY DIFFRACTIONt_it11829HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion13.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion885SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13261SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2647 479 4.97 %
Rwork0.2485 9164 -
all0.2493 9643 -
obs--96.07 %
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)
10.19130.3424-0.2470.4145-0.18290.8016-0.08830.0013-0.0312-0.05490.0140.00740.2221-0.05030.0743-0.04470.01630.0126-0.0420.0074-0.0234-3.3235-2.99-19.4267
20.26930.3874-0.19570.4811-0.26910.7530.073-0.0073-0.0440.1162-0.0566-0.02-0.00760.0349-0.0164-0.04780.0095-0.0043-0.01970.019-0.04484.18521.861719.6942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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