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- PDB-1xxi: ADP Bound E. coli Clamp Loader Complex -

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Basic information

Entry
Database: PDB / ID: 1xxi
TitleADP Bound E. coli Clamp Loader Complex
Components
  • (DNA polymerase III, delta ...) x 2
  • DNA polymerase III subunit gamma
KeywordsTRANSFERASE / AAA+ ATPase / clamp loader / DNA polymerase III / DNA replication
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 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 / DNA polymerase III, delta subunit / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / ClpA/B family / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / 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: 4.1 Å
AuthorsKazmirski, S.L. / Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex
Authors: Kazmirski, S.L. / Podobnik, M. / Weitze, T.F. / O'donnell, M. / Kuriyan, J.
History
DepositionNov 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III, delta subunit
B: DNA polymerase III subunit gamma
C: DNA polymerase III subunit gamma
D: DNA polymerase III subunit gamma
E: DNA polymerase III, delta prime subunit
F: DNA polymerase III, delta subunit
G: DNA polymerase III subunit gamma
H: DNA polymerase III subunit gamma
I: DNA polymerase III subunit gamma
J: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)398,75322
Polymers396,85310
Non-polymers1,90012
Water00
1
A: DNA polymerase III, delta subunit
B: DNA polymerase III subunit gamma
C: DNA polymerase III subunit gamma
D: DNA polymerase III subunit gamma
E: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,63812
Polymers198,4275
Non-polymers1,2117
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18380 Å2
ΔGint-89 kcal/mol
Surface area77720 Å2
MethodPISA
2
F: DNA polymerase III, delta subunit
G: DNA polymerase III subunit gamma
H: DNA polymerase III subunit gamma
I: DNA polymerase III subunit gamma
J: DNA polymerase III, delta prime subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,11510
Polymers198,4275
Non-polymers6895
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17190 Å2
ΔGint-76 kcal/mol
Surface area77780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.208, 106.574, 535.829
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThere are 2 clamp loader complexes in the asymmetric unit. One consists of chains A-E and the second consists of chains F-J

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Components

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DNA polymerase III, delta ... , 2 types, 4 molecules AFEJ

#1: Protein DNA polymerase III, delta subunit


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


Mass: 36980.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holB / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase

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Protein , 1 types, 6 molecules BCDGHI

#2: Protein
DNA polymerase III subunit gamma


Mass: 40900.172 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaX, dnaZ, dnaZX / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase

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Non-polymers , 3 types, 12 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 3.62 Å3/Da / Density % sol: 65.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.95
Details: PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2003
RadiationMonochromator: Double Crystal SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→100 Å / Num. obs: 45400 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 4.1→4.2 Å / % possible all: 83.5

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1JR3

1jr3


Resolution: 4.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.369 3986 Random
Rwork0.366 --
obs-42248 -
Refinement stepCycle: LAST / Resolution: 4.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27594 0 94 0 27688

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