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

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Basic information

Entry
Database: PDB / ID: 3aiz
TitleCrystal structure of PCNA2-PCNA3 complex from Sulfolobus tokodaii (P21212)
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 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 B
B: DNA polymerase sliding clamp B
C: DNA polymerase sliding clamp C
D: DNA polymerase sliding clamp C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,64510
Polymers110,0684
Non-polymers5766
Water73941
1
A: DNA polymerase sliding clamp B
C: DNA polymerase sliding clamp C
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)110,83712
Polymers110,0684
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2
B: DNA polymerase sliding clamp B
D: DNA polymerase sliding clamp C
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)110,4538
Polymers110,0684
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)91.110, 160.570, 116.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA polymerase sliding clamp B / PCNA2 / Proliferating cell nuclear antigen homolog B / PCNA B


Mass: 27574.600 Da / Num. of mol.: 2
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
#2: Protein DNA polymerase sliding clamp C / PCNA3 / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27459.635 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.87 Å3/Da / Density % sol: 68.24 % / Mosaicity: 0.57 °
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Feb 26, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→49.095 Å / Num. all: 42314 / Num. obs: 42314 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 49.65 Å2 / Rsym value: 0.135 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 6051 / Rsym value: 0.449 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 37.23 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å48.64 Å
Translation2.8 Å48.64 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AIX

3aix


Resolution: 2.8→48.64 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU ML: 0.34 / Isotropic thermal model: Isotropic / σ(F): 1.34 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2563 2136 5.05 %RANDOM
Rwork0.2231 40122 --
obs0.2248 42258 98.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.688 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 121.93 Å2 / Biso mean: 52.698 Å2 / Biso min: 25.51 Å2
Baniso -1Baniso -2Baniso -3
1--15.9592 Å20 Å20 Å2
2--3.6714 Å20 Å2
3---12.2878 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7738 0 30 41 7809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027881
X-RAY DIFFRACTIONf_angle_d0.47210670
X-RAY DIFFRACTIONf_dihedral_angle_d11.3362910
X-RAY DIFFRACTIONf_chiral_restr0.0321263
X-RAY DIFFRACTIONf_plane_restr0.0021354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.34882220.2863914X-RAY DIFFRACTION98
2.9001-3.01620.3182140.26883924X-RAY DIFFRACTION98
3.0162-3.15340.31891910.26173985X-RAY DIFFRACTION98
3.1534-3.31970.26781950.24533973X-RAY DIFFRACTION99
3.3197-3.52760.26482190.22683971X-RAY DIFFRACTION98
3.5276-3.79990.26142100.22414011X-RAY DIFFRACTION99
3.7999-4.18210.22352050.20944016X-RAY DIFFRACTION99
4.1821-4.78680.20352190.17394040X-RAY DIFFRACTION99
4.7868-6.0290.23532330.19784072X-RAY DIFFRACTION99
6.029-48.64770.25342280.22344216X-RAY DIFFRACTION98

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