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- PDB-3glh: Crystal Structure of the E. coli clamp loader bound to Psi Peptide -

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Basic information

Entry
Database: PDB / ID: 3glh
TitleCrystal Structure of the E. coli clamp loader bound to Psi Peptide
Components
  • DNA polymerase III subunit delta
  • DNA polymerase III subunit delta'
  • DNA polymerase III subunit tau
KeywordsTRANSFERASE / Clamp Loader / Gamma Complex / Replication / Psi / DNA replication / DNA-directed DNA polymerase / Nucleotidyltransferase / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / viral translational frameshifting / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / DNA polymerase III, delta subunit ...DNA polymerase III, delta prime subunit / DNA polymerase III, delta subunit, C-terminal / : / DNA polymerase III, delta subunit, C terminal / DNA polymerase III subunit delta', AAA+ ATPase lid domain / DNA polymerase III subunit delta, C-terminal / Processivity clamp loader gamma complex DNA pol III C-term / DNA polymerase III, delta subunit / DNA polymerase III delta, N-terminal / DNA polymerase III, delta subunit / DNA polymerase III, tau subunit, domain V / DNA polymerase III subunit tau, DnaB-binding domain IV / DNA polymerase III, tau subunit, domain V superfamily / DNA polymerase III subunits tau domain IV DnaB-binding / DNA polymerase III tau subunit V interacting with alpha / DNA polymerase III, subunit gamma/tau, helical lid domain / DNA polymerase III clamp loader subunit, ATPase lid domain / DNA polymerase III, subunit gamma/ tau, N-terminal / DNA polymerase III, gamma subunit, domain III / DNA polymerase III subunits gamma and tau domain III / Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / Ubiquitin-associated (UBA) domain / DNA polymerase III, delta subunit / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ClpA/B family / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit tau / DNA polymerase III subunit delta / DNA polymerase III subunit delta'
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.891 Å
AuthorsKazmirski, S.L. / Simonetta, K.R. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: The mechanism of ATP-dependent primer-template recognition by a clamp loader complex.
Authors: Simonetta, K.R. / Kazmirski, S.L. / Goedken, E.R. / Cantor, A.J. / Kelch, B.A. / McNally, R. / Seyedin, S.N. / Makino, D.L. / O'Donnell, M. / Kuriyan, J.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'
K: DNA polymerase III subunit delta
L: DNA polymerase III subunit tau
M: DNA polymerase III subunit tau
N: DNA polymerase III subunit tau
O: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)603,40715
Polymers603,40715
Non-polymers00
Water00
1
A: DNA polymerase III subunit delta
B: DNA polymerase III subunit tau
C: DNA polymerase III subunit tau
D: DNA polymerase III subunit tau
E: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15990 Å2
ΔGint-64 kcal/mol
Surface area79710 Å2
MethodPISA
2
F: DNA polymerase III subunit delta
G: DNA polymerase III subunit tau
H: DNA polymerase III subunit tau
I: DNA polymerase III subunit tau
J: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-60 kcal/mol
Surface area79520 Å2
MethodPISA
3
K: DNA polymerase III subunit delta
L: DNA polymerase III subunit tau
M: DNA polymerase III subunit tau
N: DNA polymerase III subunit tau
O: DNA polymerase III subunit delta'


Theoretical massNumber of molelcules
Total (without water)201,1365
Polymers201,1365
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16160 Å2
ΔGint-65 kcal/mol
Surface area78830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.162, 228.494, 164.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA polymerase III subunit delta


Mass: 38745.574 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holA, b0640, JW0635 / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase
#2: Protein
DNA polymerase III subunit tau / DNA polymerase III subunit gamma


Mass: 41803.168 Da / Num. of mol.: 9 / Fragment: UNP residues 1-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: dnaX, dnaZ, dnaZX, b0470, JW0459 / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase
#3: Protein DNA polymerase III subunit delta'


Mass: 36980.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: holB, b1099, JW1085 / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase

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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: 3.03 Å3/Da / Density % sol: 59.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 300 mM NaK Tartrate, 10% PEG 3350, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2004
RadiationMonochromator: KOHZU / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.891→100 Å / Num. all: 67070 / Num. obs: 65729 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.891→3.99 Å / % possible all: 94.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.891→49.621 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.87 / σ(F): 0.03 / Phase error: 41.25 / Stereochemistry target values: ML
Details: There are several close contacts because this structure is only a 4A structure
RfactorNum. reflection% reflectionSelection details
Rfree0.3614 5893 4.9 %Random
Rwork0.3593 ---
obs-64229 89.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.525 Å2 / ksol: 0.309 e/Å3
Displacement parametersBiso max: 291.12 Å2 / Biso mean: 111.018 Å2 / Biso min: 29.92 Å2
Baniso -1Baniso -2Baniso -3
1-94.7798 Å20 Å217.6454 Å2
2--93.89 Å2-0 Å2
3---64.4952 Å2
Refinement stepCycle: LAST / Resolution: 3.891→49.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41322 0 0 0 41322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01442069
X-RAY DIFFRACTIONf_angle_d1.7957096
X-RAY DIFFRACTIONf_dihedral_angle_d19.51115639
X-RAY DIFFRACTIONf_chiral_restr0.1256648
X-RAY DIFFRACTIONf_plane_restr0.0117410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.891-3.93560.4643920.44421902X-RAY DIFFRACTION44
3.9356-3.98190.44741510.42383114X-RAY DIFFRACTION75
3.9819-4.03050.42061770.42913172X-RAY DIFFRACTION75
4.0305-4.08140.48411920.41953282X-RAY DIFFRACTION78
4.0814-4.13510.39861720.42033407X-RAY DIFFRACTION80
4.1351-4.19170.44261630.40613534X-RAY DIFFRACTION82
4.1917-4.25160.38071870.40673514X-RAY DIFFRACTION84
4.2516-4.3150.42071790.38253638X-RAY DIFFRACTION85
4.315-4.38240.41821750.3973638X-RAY DIFFRACTION85
4.3824-4.45420.3922310.39273690X-RAY DIFFRACTION88
4.4542-4.5310.37281760.38883862X-RAY DIFFRACTION90
4.531-4.61330.37911640.38173820X-RAY DIFFRACTION90
4.6133-4.7020.37322330.37693874X-RAY DIFFRACTION92
4.702-4.79790.35911910.37513942X-RAY DIFFRACTION92
4.7979-4.90210.3561840.37163940X-RAY DIFFRACTION93
4.9021-5.0160.34141920.38874044X-RAY DIFFRACTION94
5.016-5.14140.34622440.39113935X-RAY DIFFRACTION94
5.1414-5.28020.33592010.38314071X-RAY DIFFRACTION95
5.2802-5.43540.38632260.39364024X-RAY DIFFRACTION96
5.4354-5.61060.38161740.39054078X-RAY DIFFRACTION97
5.6106-5.81080.3982190.37814170X-RAY DIFFRACTION97
5.8108-6.04310.42012210.39034122X-RAY DIFFRACTION98
6.0431-6.31760.34762060.37984209X-RAY DIFFRACTION99
6.3176-6.650.41232120.36964281X-RAY DIFFRACTION99
6.65-7.06550.36442210.35944160X-RAY DIFFRACTION99
7.0655-7.60930.33122400.33144207X-RAY DIFFRACTION100
7.6093-8.37170.25281900.29524298X-RAY DIFFRACTION100
8.3717-9.57560.23972140.26894202X-RAY DIFFRACTION99
9.5756-12.03570.26722370.24664138X-RAY DIFFRACTION99
12.0357-49.6250.37462290.3094224X-RAY DIFFRACTION99

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