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- PDB-1b8h: SLIDING CLAMP, DNA POLYMERASE -

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Basic information

Entry
Database: PDB / ID: 1b8h
TitleSLIDING CLAMP, DNA POLYMERASE
Components
  • DNA POLYMERASE PROCESSIVITY COMPONENT
  • DNA POLYMERASE fragment
KeywordsTRANSFERASE / SLIDING CLAMP / GP45 / REPLISOME / ACCESSORY PROTEIN
Function / homology
Function and homology information


bidirectional double-stranded viral DNA replication / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / DNA polymerase processivity factor activity / viral transcription / SOS response / 3'-5' exonuclease activity ...bidirectional double-stranded viral DNA replication / viral DNA genome replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / DNA polymerase processivity factor activity / viral transcription / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding
Similarity search - Function
Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / DNA-directed DNA polymerase T4 type / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase family B signature. ...Sliding clamp, C-terminal / Sliding clamp / gp45 sliding clamp, C terminal / DNA polymerase processivity factor / DNA polymerase processivity factor / DNA-directed DNA polymerase T4 type / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, conserved site / : / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
Sliding clamp / DNA-directed DNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage RB69 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionFeb 1, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE PROCESSIVITY COMPONENT
B: DNA POLYMERASE PROCESSIVITY COMPONENT
C: DNA POLYMERASE PROCESSIVITY COMPONENT
D: DNA POLYMERASE fragment


Theoretical massNumber of molelcules
Total (without water)76,7514
Polymers76,7514
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-23 kcal/mol
Surface area32630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.000, 90.500, 146.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.92414, 0.22872, 0.30601), (0.37944, -0.45603, -0.80502), (-0.04457, 0.86007, -0.50822)-56.2807, 190.87675, 169.31078
2given(0.91465, 0.37511, -0.15069), (0.31395, -0.42429, 0.84936), (0.25467, -0.82418, -0.50584)2.8028, -46.58457, 259.63107

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Components

#1: Protein DNA POLYMERASE PROCESSIVITY COMPONENT / GP45 / DNA Polymerase Sliding clamp / DNA POLYMERASE ACCESSORY PROTEIN 45


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: Protein/peptide DNA POLYMERASE fragment / GP43


Mass: 1350.581 Da / Num. of mol.: 1 / Fragment: RESIDUES 893-903 / Source method: obtained synthetically / Details: SEQUENCE FROM BACTERIOPHAGE RB69, GENE 43 / References: UniProt: Q38087

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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 growMethod: vapor diffusion, hanging drop / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2calcium acetate11
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: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 15, 1998 / Details: YALE MIRRORS
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 18527 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 0.105 / Net I/σ(I): 10.6
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 47361 / Rmerge(I) obs: 0.105

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B77

1b77


Resolution: 3→40 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 106093.96 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: B FACTORS FROM 1B77
RfactorNum. reflection% reflectionSelection details
Rfree0.313 1695 9.9 %RANDOM
Rwork0.265 ---
all-17061 --
obs-17061 92.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5393 0 0 0 5393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.82
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.531.5
X-RAY DIFFRACTIONx_mcangle_it0.962
X-RAY DIFFRACTIONx_scbond_it0.842
X-RAY DIFFRACTIONx_scangle_it1.312.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 286 11 %
Rwork0.345 2317 -
obs--86 %
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
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.271
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.399 / % reflection Rfree: 11 % / Rfactor Rwork: 0.345

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