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- PDB-1b77: BUILDING A REPLISOME STRUCTURE FROM INTERACTING PIECES: A SLIDING... -

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Basic information

Entry
Database: PDB / ID: 1b77
TitleBUILDING A REPLISOME STRUCTURE FROM INTERACTING PIECES: A SLIDING CLAMP COMPLEXED WITH AN INTERACTION PEPTIDE FROM DNA POLYMERASE
ComponentsPROTEIN (SLIDING CLAMP)
KeywordsSLIDING CLAMP / GP45 / REPLISOME
Function / homology
Function and homology information


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 RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShamoo, Y. / Steitz, T.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
Authors: Shamoo, Y. / Steitz, T.A.
History
DepositionJan 27, 1999Processing site: RCSB
Revision 1.0Feb 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (SLIDING CLAMP)
B: PROTEIN (SLIDING CLAMP)
C: PROTEIN (SLIDING CLAMP)


Theoretical massNumber of molelcules
Total (without water)75,4003
Polymers75,4003
Non-polymers00
Water12,845713
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.900, 87.600, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.93819, 0.2581, 0.23062), (0.32837, -0.45311, -0.82877), (-0.10941, 0.85328, -0.50985)-44.94521, 187.2319, 163.21458
2given(0.92134, 0.33923, -0.18987), (0.33229, -0.43375, 0.83752), (0.20176, -0.83474, -0.51235)9.89061, -42.47113, 250.70518

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Components

#1: Protein PROTEIN (SLIDING CLAMP) / GP45


Mass: 25133.475 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage RB69 (virus) / Genus: T4-like viruses / Gene: GENE 45 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: O80164
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2.8 Å3/Da / Density % sol: 47 %
Crystal growpH: 7.5 / Details: 16-18% PEG 8000, 0.2 M CA ACETATE PH7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17.5 mg/mlprotein1drop
28-9 %(w/v)PEG80001drop
30.1 Mcalcium acetate1drop
40.1 MHEPES1drop
516-18 %(w/v)PEG80001reservoir
60.2 Mcalcium acetate1reservoir
70.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9188
DetectorType: ADSC / Detector: CCD / Date: Nov 1, 1997 / Details: SILICON 111 BENDING MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 47361 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 15 Å2 / Rsym value: 0.07 / Net I/σ(I): 6.6
Reflection
*PLUS
Num. measured all: 151555 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PRELIMINARY COORDINATE OF T4 GP45 FROM J. KURIYAN

Resolution: 2.1→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high rms absF: 347237.93 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4506 10 %RANDOM
Rwork0.225 ---
obs-45020 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.02 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20 Å2
2--1.85 Å20 Å2
3----4.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 0 713 6011
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.541.5
X-RAY DIFFRACTIONx_mcangle_it0.972
X-RAY DIFFRACTIONx_scbond_it0.852
X-RAY DIFFRACTIONx_scangle_it1.322.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 667 10.1 %
Rwork0.293 5930 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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