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- PDB-4tr8: Crystal structure of DNA polymerase sliding clamp from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 4tr8
TitleCrystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa
ComponentsDNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsDNA BINDING PROTEIN / DNA polymerase / sliding clamp / processivity
Function / homology
Function and homology information


DNA polymerase III complex / 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 / 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 ...DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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
Beta sliding clamp / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa HB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 15, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Other

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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)85,1203
Polymers85,0972
Non-polymers231
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-12 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.530, 92.410, 127.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA polymerase III subunit beta / DNA polymerase III holoenzyme


Mass: 42548.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa HB15 (bacteria) / Gene: PA15_0320650 / Production host: Escherichia coli (E. coli)
References: UniProt: V4MZL6, UniProt: Q9I7C4*PLUS, 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 / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.79 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1M sodium acetate pH 4.5 and PEG 3350 / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→43.9 Å / Num. obs: 88854 / % possible obs: 99.6 % / Redundancy: 14.7 % / Biso Wilson estimate: 27.18 Å2 / Net I/σ(I): 17.69

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→43.9 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9296 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.116 / SU Rfree Blow DPI: 0.109 / SU Rfree Cruickshank DPI: 0.108
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 4437 5.01 %RANDOM
Rwork0.2074 ---
obs0.2086 88625 99.98 %-
Displacement parametersBiso mean: 34.57 Å2
Baniso -1Baniso -2Baniso -3
1--3.2454 Å20 Å20 Å2
2--5.5899 Å20 Å2
3----2.3444 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: 1 / Resolution: 1.8→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5556 0 1 432 5989
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015634HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.117655HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1968SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes146HARMONIC2
X-RAY DIFFRACTIONt_gen_planes837HARMONIC5
X-RAY DIFFRACTIONt_it5634HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion16.24
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion751SEMIHARMONIC5
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_contact6592SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3107 315 4.86 %
Rwork0.2904 6167 -
all0.2914 6482 -
obs--99.98 %
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)
10.4817-0.26480.28321.2249-0.24590.2782-0.05670.03280.02160.0979-0.0069-0.1262-0.09090.0130.0637-0.0538-0.00330.0191-0.0506-0.0193-0.0559-17.63737.7039-30.6066
20.0748-0.07240.27362.35280.16940.25130.0230.0019-0.0648-0.65190.02710.1976-0.01480.0118-0.050.0492-0.02870.006-0.10820.0114-0.1209-39.3429-14.9245-54.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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