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- PDB-3aix: Crystal structure of PCNA2-PCNA3 complex from Sulfolobus tokodaii... -

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Basic information

Entry
Database: PDB / ID: 3aix
TitleCrystal structure of PCNA2-PCNA3 complex from Sulfolobus tokodaii (I222)
Components
  • DNA polymerase sliding clamp B
  • DNA polymerase sliding clamp C
KeywordsREPLICATION / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / : / Alpha Beta
Similarity search - Domain/homology
DNA polymerase sliding clamp 3 / DNA polymerase sliding clamp 2
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsKawai, A. / Higuchi, S. / Miyamoto, S.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: A novel heterotetrameric structure of the crenarchaeal PCNA2-PCNA3 complex
Authors: Kawai, A. / Hashimoto, H. / Higuchi, S. / Tsunoda, M. / Sato, M. / Nakamura, K.T. / Miyamoto, S.
History
DepositionMay 18, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA polymerase sliding clamp C
B: DNA polymerase sliding clamp B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3225
Polymers55,0342
Non-polymers2883
Water46826
1
A: DNA polymerase sliding clamp C
B: DNA polymerase sliding clamp B
hetero molecules

A: DNA polymerase sliding clamp C
B: DNA polymerase sliding clamp B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,64510
Polymers110,0684
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Unit cell
Length a, b, c (Å)91.100, 111.800, 170.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DNA polymerase sliding clamp C / PCNA3 / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27459.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: st0944 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q973F5
#2: Protein DNA polymerase sliding clamp B / PCNA2 / Proliferating cell nuclear antigen homolog B / PCNA B


Mass: 27574.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: st0397 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q975M2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.95 Å3/Da / Density % sol: 68.89 % / Mosaicity: 1.02 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M ammonium sulfate, 0.1M sodium Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→93.549 Å / Num. all: 19736 / Num. obs: 19736 / % possible obs: 100 % / Redundancy: 10.7 % / Biso Wilson estimate: 52.6 Å2 / Rsym value: 0.101 / Net I/σ(I): 19.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 2830 / Rsym value: 0.495 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å48.3 Å
Translation2.9 Å48.3 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IZO

2izo


Resolution: 2.9→48.301 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.821 / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.38 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1009 5.12 %RANDOM
Rwork0.2098 18709 --
obs0.2123 19718 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.352 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 105.19 Å2 / Biso mean: 47.577 Å2 / Biso min: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1--5.4053 Å20 Å20 Å2
2--4.5194 Å20 Å2
3---0.8858 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 15 26 3905
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023935
X-RAY DIFFRACTIONf_angle_d0.475327
X-RAY DIFFRACTIONf_dihedral_angle_d9.8691452
X-RAY DIFFRACTIONf_chiral_restr0.031631
X-RAY DIFFRACTIONf_plane_restr0.002675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8999-3.05280.33841500.27682617X-RAY DIFFRACTION100
3.0528-3.2440.30821330.25132639X-RAY DIFFRACTION100
3.244-3.49440.24711570.21892650X-RAY DIFFRACTION100
3.4944-3.8460.27061390.20632649X-RAY DIFFRACTION100
3.846-4.40220.24311420.19782660X-RAY DIFFRACTION100
4.4022-5.5450.22141330.16492713X-RAY DIFFRACTION100
5.545-48.30740.23431550.21132781X-RAY DIFFRACTION99

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