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- PDB-3lx2: Crystal Structure analysis of PCNA from Thermococcus kodakaraensi... -

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Basic information

Entry
Database: PDB / ID: 3lx2
TitleCrystal Structure analysis of PCNA from Thermococcus kodakaraensis tk0582
ComponentsDNA polymerase sliding clamp 2
KeywordsDNA BINDING PROTEIN / PCNA / DNA processivity factor / trimer / toroidal / DNA replication / DNA-binding
Function / homology
Function and homology information


leading strand elongation / DNA polymerase processivity factor activity / regulation of DNA replication / DNA binding / identical protein 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 2
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsLadner, J.E. / Kelman, Z. / Pan, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structures of two active proliferating cell nuclear antigens (PCNAs) encoded by Thermococcus kodakaraensis.
Authors: Ladner, J.E. / Pan, M. / Hurwitz, J. / Kelman, Z.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 2
B: DNA polymerase sliding clamp 2
C: DNA polymerase sliding clamp 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5009
Polymers87,9243
Non-polymers5766
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-80 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.480, 136.270, 123.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein DNA polymerase sliding clamp 2 / Proliferating cell nuclear antigen homolog 2 / PCNA 2


Mass: 29307.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: pcn2, tk0535, TK0582 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta / References: UniProt: Q5JFD3
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 2.4-2.8 M ammonium sulfate, 100 mM sodium citrate, 5-10% 2,4-methyl pentanediol. The protein solution has 10% glycerol, VAPOR DIFFUSION, temperature 295K
PH range: 5.2-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→29.86 Å / Num. obs: 36454 / % possible obs: 90.8 % / Redundancy: 2.83 % / Rmerge(I) obs: 0.039 / Χ2: 0.97 / Net I/σ(I): 13.4 / Scaling rejects: 781
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.4-2.492.720.3452.7956935051.1289
2.49-2.592.760.2973973435151.188.6
2.59-2.72.80.2433.5988035171.0688.5
2.7-2.852.820.1894.3985234821.0487.1
2.85-3.022.850.126.51000735010.9687.5
3.02-3.262.870.0858.91017835410.9289
3.26-3.582.840.05812.31059737130.8292.9
3.58-4.12.770.04717.81046637190.9692.3
4.1-5.162.910.02828.81170039920.8698.5
5.16-29.632.960.02237.81209739690.9494.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.63 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.303 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.718 / SU B: 11.389 / SU ML: 0.266 / SU R Cruickshank DPI: 0.468 / SU Rfree: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1798 5 %RANDOM
Rwork0.243 ---
obs0.246 35927 89.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.16 Å2 / Biso mean: 57.023 Å2 / Biso min: 28.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---2.28 Å20 Å2
3---0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5851 0 30 71 5952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225980
X-RAY DIFFRACTIONr_angle_refined_deg1.7961.9978089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1685736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.90524.118255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.45151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1521539
X-RAY DIFFRACTIONr_chiral_restr0.1170.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214369
X-RAY DIFFRACTIONr_mcbond_it0.9651.53689
X-RAY DIFFRACTIONr_mcangle_it1.80325964
X-RAY DIFFRACTIONr_scbond_it2.55932291
X-RAY DIFFRACTIONr_scangle_it4.2954.52125
LS refinement shellResolution: 2.4→2.529 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.49 253 -
Rwork0.327 4744 -
all-4997 -
obs--86.69 %

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