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- PDB-1czd: CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4 -

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Basic information

Entry
Database: PDB / ID: 1czd
TitleCRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4
ComponentsDNA POLYMERASE ACCESSORY PROTEIN G45
KeywordsGENE REGULATION / BACTERIOPHAGE T4 / PROCESSIVITY CLAMP / DNA REPLICATION / RING-SHAPED PROTEIN
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / viral DNA genome replication / DNA polymerase processivity factor activity / viral transcription / DNA replication
Similarity search - Function
Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / : / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsMoarefi, I. / Jeruzalmi, D. / Turner, J. / O'Donnell, M. / Kuriyan, J.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage.
Authors: Moarefi, I. / Jeruzalmi, D. / Turner, J. / O'Donnell, M. / Kuriyan, J.
History
DepositionSep 2, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE ACCESSORY PROTEIN G45
B: DNA POLYMERASE ACCESSORY PROTEIN G45
C: DNA POLYMERASE ACCESSORY PROTEIN G45


Theoretical massNumber of molelcules
Total (without water)74,6443
Polymers74,6443
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-18 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.177, 93.938, 141.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a trimer constructed from residues 1001 to 1228 by a three-fold NCS operation.

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Components

#1: Protein DNA POLYMERASE ACCESSORY PROTEIN G45


Mass: 24881.223 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Production host: Escherichia coli (E. coli) / References: UniProt: P04525

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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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 60 mM PIPES 200 mM CASO4 0.1 % 1,4 Dioxane 15% Glycerol 15% PEG MME 5000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
160 mMPIPES1reservoir
2200 mM1reservoirCaSO4
30.1 %(v/v)1,4-dioxane1reservoir
415 %(v/v)glycerol1reservoir
515 %(v/v)PEG5000 MME1reservoir
60.1 mMPHMB1drop
710 mMTris1drop

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.45→100 Å / Num. all: 30934 / Num. obs: 28409 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 15.6
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.29 / Num. unique all: 2975 / % possible all: 95.4
Reflection
*PLUS
Num. obs: 30934 / Num. measured all: 282837
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.29

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.45→100 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood (MLF) target in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 --Random
Rwork0.232 ---
all-30934 --
obs-28409 92.5 %-
Refinement stepCycle: LAST / Resolution: 2.45→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5250 0 0 0 5250
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.29315
X-RAY DIFFRACTIONc_bond_d0.007106
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 2 / Rfactor obs: 0.2322
Solvent computation
*PLUS
Displacement parameters
*PLUS

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