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- PDB-4tr7: Crystal structure of DNA polymerase sliding clamp from Mycobateri... -

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Basic information

Entry
Database: PDB / ID: 4tr7
TitleCrystal structure of DNA polymerase sliding clamp from Mycobaterium tuberculosis
ComponentsDNA polymerase III subunit beta
KeywordsDNA BINDING PROTEIN / sliding clamp / processivity
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
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 / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / : / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsOlieric, V. / Burnouf, D. / 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)84,3022
Polymers84,3022
Non-polymers00
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-9 kcal/mol
Surface area33080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.490, 83.650, 84.030
Angle α, β, γ (deg.)63.58, 86.84, 85.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA polymerase III subunit beta


Mass: 42150.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: dnaN, MT0002 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WNU0, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.01 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.2M sodium acetate trihydrate pH 7.0 and 20% PEG 3350
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→36.4 Å / Num. obs: 42571 / % possible obs: 96.4 % / Redundancy: 3.93 % / Biso Wilson estimate: 47.28 Å2 / Net I/σ(I): 19.53

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→18.76 Å / Cor.coef. Fo:Fc: 0.9108 / Cor.coef. Fo:Fc free: 0.8895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.227 / SU Rfree Blow DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2379 2152 5.06 %RANDOM
Rwork0.2023 ---
obs0.2041 42529 96.15 %-
Displacement parametersBiso mean: 52.87 Å2
Baniso -1Baniso -2Baniso -3
1--22.8595 Å2-9.1779 Å23.194 Å2
2--11.3346 Å23.7272 Å2
3---11.5249 Å2
Refine analyzeLuzzati coordinate error obs: 0.343 Å
Refinement stepCycle: 1 / Resolution: 2.29→18.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10445 0 0 217 10662
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110532HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1619103HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2243SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes90HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1578HARMONIC5
X-RAY DIFFRACTIONt_it10532HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion14.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion758SEMIHARMONIC5
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_contact11133SEMIHARMONIC4
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3022 149 5.45 %
Rwork0.2371 2587 -
all0.2409 2736 -
obs--96.15 %
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)
1-0.01020.028-0.03021.96151.56261.59520.06440.0142-0.0227-0.4393-0.09670.003-0.3998-0.11280.0323-0.01950.0650.0012-0.09130.0283-0.0921-5.997216.0366-11.1738
20.0858-0.1840.20961.59261.23061.42010.01570.05790.010.23180.1419-0.12440.23120.1996-0.1576-0.0411-0.00220.0065-0.08850.0183-0.08675.7943-15.500511.1381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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