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

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Basic information

Entry
Database: PDB / ID: 4tsz
TitleCrystal structure of DNA polymerase sliding clamp from Pseudomonas aeruginosa with ligand
Components
  • ACE-GLN-ALC-ASP-LEU-ZCL peptide
  • DNA polymerase III subunit betaDNA polymerase III holoenzyme
KeywordsTRANSFERASE
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
peptide ligand / Beta sliding clamp / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references / Derived calculations / Structure summary
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Dec 21, 2016Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III subunit beta
Q: ACE-GLN-ALC-ASP-LEU-ZCL peptide
B: DNA polymerase III subunit beta
R: ACE-GLN-ALC-ASP-LEU-ZCL peptide
C: DNA polymerase III subunit beta
S: ACE-GLN-ALC-ASP-LEU-ZCL peptide
D: DNA polymerase III subunit beta
T: ACE-GLN-ALC-ASP-LEU-ZCL peptide
E: DNA polymerase III subunit beta
U: ACE-GLN-ALC-ASP-LEU-ZCL peptide
F: DNA polymerase III subunit beta
V: ACE-GLN-ALC-ASP-LEU-ZCL peptide
G: DNA polymerase III subunit beta
X: ACE-GLN-ALC-ASP-LEU-ZCL peptide
H: DNA polymerase III subunit beta
Y: ACE-GLN-ALC-ASP-LEU-ZCL peptide
I: DNA polymerase III subunit beta
Z: ACE-GLN-ALC-ASP-LEU-ZCL peptide
J: DNA polymerase III subunit beta
0: ACE-GLN-ALC-ASP-LEU-ZCL peptide
K: DNA polymerase III subunit beta
1: ACE-GLN-ALC-ASP-LEU-ZCL peptide
L: DNA polymerase III subunit beta
2: ACE-GLN-ALC-ASP-LEU-ZCL peptide
M: DNA polymerase III subunit beta
3: ACE-GLN-ALC-ASP-LEU-ZCL peptide
N: DNA polymerase III subunit beta
4: ACE-GLN-ALC-ASP-LEU-ZCL peptide
O: DNA polymerase III subunit beta
5: ACE-GLN-ALC-ASP-LEU-ZCL peptide
P: DNA polymerase III subunit beta
6: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)666,35532
Polymers666,35532
Non-polymers00
Water44,2812458
1
C: DNA polymerase III subunit beta
S: ACE-GLN-ALC-ASP-LEU-ZCL peptide
D: DNA polymerase III subunit beta
T: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA polymerase III subunit beta
Q: ACE-GLN-ALC-ASP-LEU-ZCL peptide
B: DNA polymerase III subunit beta
R: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: DNA polymerase III subunit beta
U: ACE-GLN-ALC-ASP-LEU-ZCL peptide
F: DNA polymerase III subunit beta
V: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: DNA polymerase III subunit beta
X: ACE-GLN-ALC-ASP-LEU-ZCL peptide
H: DNA polymerase III subunit beta
Y: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: DNA polymerase III subunit beta
Z: ACE-GLN-ALC-ASP-LEU-ZCL peptide
J: DNA polymerase III subunit beta
0: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: DNA polymerase III subunit beta
1: ACE-GLN-ALC-ASP-LEU-ZCL peptide
L: DNA polymerase III subunit beta
2: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
M: DNA polymerase III subunit beta
3: ACE-GLN-ALC-ASP-LEU-ZCL peptide
N: DNA polymerase III subunit beta
4: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
O: DNA polymerase III subunit beta
5: ACE-GLN-ALC-ASP-LEU-ZCL peptide
P: DNA polymerase III subunit beta
6: ACE-GLN-ALC-ASP-LEU-ZCL peptide


Theoretical massNumber of molelcules
Total (without water)83,2944
Polymers83,2944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.982, 85.947, 272.202
Angle α, β, γ (deg.)90.01, 89.94, 116.56
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA polymerase III subunit beta / DNA polymerase III holoenzyme / DNA polymerase sliding clamp from Pseudomonas aeruginosa


Mass: 40877.504 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: V4MZL6, UniProt: Q9I7C4*PLUS, DNA-directed DNA polymerase
#2: Protein/peptide
ACE-GLN-ALC-ASP-LEU-ZCL peptide


Type: Oligopeptide / Class: Inhibitor / Mass: 769.713 Da / Num. of mol.: 16 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: peptide ligand
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2458 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE SHORT PEPTIDE BINDS ONTO PROCESSIVITY FACTOR BETA CLAMP, INHIBITING BETA-DEPENDENT ELONGATION ACTIVITY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 44.1 %
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: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.3 Å / Num. obs: 787947 / % possible obs: 87.9 % / Redundancy: 1.6 % / Biso Wilson estimate: 39.48 Å2 / Net I/σ(I): 6.12
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.55 % / Mean I/σ(I) obs: 0.75 / % possible all: 75.3

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9412 / SU R Cruickshank DPI: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.179 / SU Rfree Blow DPI: 0.147 / SU Rfree Cruickshank DPI: 0.15
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 21173 5.03 %RANDOM
Rwork0.2019 ---
obs0.2029 421275 96.21 %-
Displacement parametersBiso mean: 48.85 Å2
Baniso -1Baniso -2Baniso -3
1-4.6397 Å2-0.447 Å20.3875 Å2
2--0.4635 Å2-0.027 Å2
3----5.1032 Å2
Refine analyzeLuzzati coordinate error obs: 0.308 Å
Refinement stepCycle: 1 / Resolution: 2→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44370 0 2909 2460 49739
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00945440HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1161668HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d15954SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes1185HARMONIC2
X-RAY DIFFRACTIONt_gen_planes6841HARMONIC5
X-RAY DIFFRACTIONt_it45440HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5983SEMIHARMONIC5
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_contact51932SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2426 1482 5.06 %
Rwork0.229 27831 -
all0.2296 29313 -
obs--96.21 %
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)
12.0461-0.1511-0.34240.47440.01570.10950.2725-0.11860.5088-0.0427-0.1834-0.1669-0.14360.0746-0.08910.251-0.02860.09650.2335-0.0149-0.0842-0.534733.5981-103.8565
21.08660.98720.05553.19540.26440.02220.00530.04350.1411-0.1064-0.00560.1802-0.0295-0.010.0003-0.13360.03460.0036-0.1669-0.0029-0.1573-62.349243.1261-2.0195
31.2758-0.60660.23711.7229-0.22180.65740.0588-0.3823-0.2924-0.02380.12650.1790.1765-0.1726-0.1854-0.0238-0.1352-0.02830.24170.1806-0.1459-62.01844.9943100.9102
42.2788-0.1005-0.2171.15220.02220.13670.02970.0307-0.1656-0.0415-0.0504-0.27320.0151-0.00140.0208-0.12960.0247-0.0205-0.157-0.0196-0.1615-32.20218.0851-2.4376
52.2132-0.0548-0.01571.1615-0.25270.35550.1491-0.38570.3150.026-0.132-0.1749-0.150.0468-0.01710.0971-0.14120.01490.3015-0.0201-0.1004-32.007170.2004100.6265
61.3648-0.6327-0.21661.81080.2320.64180.044-0.37130.3031-0.03480.1357-0.1912-0.17670.1635-0.1796-0.0161-0.14820.0310.2216-0.1892-0.1487-31.9635-2.7469-35.1941
72.2811-0.0190.091.13610.22310.29810.1552-0.4005-0.31710.0221-0.13720.19440.1418-0.0455-0.0180.0931-0.1391-0.00820.3005-0.0019-0.1058-61.9792-27.9478-35.4429
80.9343-0.3898-0.07860.86160.01310.74450.1011-0.08770.1764-0.0072-0.0141-0.0877-0.07670.031-0.0870.0763-0.0364-0.01830.0728-0.0408-0.1987-63.349333.515732.8822
91.8771-0.03310.43360.3957-0.09430.1970.2806-0.0945-0.494-0.0522-0.18960.15970.1542-0.0655-0.09090.2548-0.03-0.08920.2236-0.0002-0.0645-93.60788.613332.2716
101.08590.4272-0.0521.1446-0.06380.01150.04340.0221-0.1286-0.0164-0.0354-0.13470.00810.001-0.0081-0.13170.0215-0.0064-0.15150.0039-0.1989-24.7833-23.061465.8354
111.24350.3887-0.01971.12120.144-0.00010.0487-0.01530.1948-0.0562-0.06630.0526-0.0171-0.00090.0177-0.11460.02680.019-0.14580.0132-0.1553-55.02461.868866.0148
121.08690.42880.01651.21440.04910.0190.05230.0160.1299-0.0086-0.04340.1431-0.0035-0.0006-0.0089-0.14340.0179-0.0071-0.1708-0.007-0.2038-69.264265.2964-70.2615
131.23250.357-0.03341.1526-0.17690.00020.0466-0.018-0.1833-0.0514-0.0705-0.05760.01510.00370.024-0.12920.0237-0.0356-0.1581-0.0167-0.1557-39.02540.3637-70.0752
142.0364-0.20750.1261.215-0.0730.10880.04820.02280.1128-0.0256-0.05830.26680.00160.00440.01-0.15170.02120.011-0.17620.0146-0.1881-61.988324.0402133.9921
151.14631.0305-0.00993.1141-0.24350.0141-0.01290.048-0.1737-0.13190.0145-0.17880.04090.0169-0.0017-0.11650.0346-0.01-0.1542-0.0037-0.1275-31.7995-0.9526133.7197
161.0105-0.45910.10330.922-0.03120.72620.0977-0.0875-0.1721-0.0021-0.0240.08960.0804-0.0298-0.07380.0762-0.03170.01330.07980.0364-0.2041-30.79068.693-103.2187
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|* }
2X-RAY DIFFRACTION2{ A|* }
3X-RAY DIFFRACTION3{ O|* }
4X-RAY DIFFRACTION4{ B|* }
5X-RAY DIFFRACTION5{ P|* }
6X-RAY DIFFRACTION6{ C|* }
7X-RAY DIFFRACTION7{ D|* }
8X-RAY DIFFRACTION8{ E|* }
9X-RAY DIFFRACTION9{ F|* }
10X-RAY DIFFRACTION10{ G|* }
11X-RAY DIFFRACTION11{ H|* }
12X-RAY DIFFRACTION12{ I|* }
13X-RAY DIFFRACTION13{ J|* }
14X-RAY DIFFRACTION14{ K|* }
15X-RAY DIFFRACTION15{ L|* }
16X-RAY DIFFRACTION16{ M|* }

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