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- PDB-1a5t: CRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER ... -

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Basic information

Entry
Database: PDB / ID: 1a5t
TitleCRYSTAL STRUCTURE OF THE DELTA PRIME SUBUNIT OF THE CLAMP-LOADER COMPLEX OF ESCHERICHIA COLI DNA POLYMERASE III
ComponentsDELTA PRIME
KeywordsZINC FINGER / DNA REPLICATION
Function / homology
Function and homology information


DNA polymerase III, clamp loader complex / DNA clamp loader activity / DNA polymerase III complex / replisome / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / 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, delta subunit / Ubiquitin-associated (UBA) domain / : ...Zinc Finger, Delta Prime; domain 3 - #10 / Zinc Finger, Delta Prime; domain 3 / 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, delta subunit / Ubiquitin-associated (UBA) domain / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / 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 delta'
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsGuenther, B. / Onrust, R. / Sali, A. / O'Donnell, M. / Kuriyan, J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III.
Authors: Guenther, B. / Onrust, R. / Sali, A. / O'Donnell, M. / Kuriyan, J.
#1: Journal: Thesis, The Rockefeller University / Year: 1996
Title: Structural Studies on the DNA Replication Apparatus: X-Ray Crystal Structure of the Delta-Prime Subunit of Escherichia Coli DNA Polymerase III
Authors: Guenther, B.D.
History
DepositionFeb 18, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

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Assembly

Deposited unit
A: DELTA PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0462
Polymers36,9801
Non-polymers651
Water3,639202
1
A: DELTA PRIME
hetero molecules

A: DELTA PRIME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0924
Polymers73,9612
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)98.900, 104.000, 75.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DELTA PRIME / HOLB


Mass: 36980.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Cellular location: CYTOPLASM / Gene: HOLB / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 277 K / pH: 6.8
Details: THE PROTEIN WAS CRYSTALLIZED FROM 20-27% PEG 400, 100 MM HEPES, PH6.8, 100 MM MGCL2, 1-3% GLYCEROL, 10MM MGSO4, AT 4C, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220-27 %PEG4001reservoir
3100 mMHEPES1reservoir
4100 mM1reservoirMgCl2
51-3 %glycerol1reservoir
610 mM1reservoirMgSO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 19389 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.074 / Net I/σ(I): 23
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 6 / Rsym value: 0.353 / % possible all: 93
Reflection
*PLUS
Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 93 % / Rmerge(I) obs: 0.353

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: INFORMATION FOR THE ZINC AND ZN-S INTERACTIONS WERE INCORPORATED INTO THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.265 -10 %RANDOM
Rwork0.205 ---
obs0.205 17778 88 %-
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 1 202 2715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.15
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8
Rfactor% reflection
Rfree0.285 6.8 %
Rwork0.233 -
obs-74.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18759 / Rfactor all: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.233

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