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- PDB-3lx1: Crystal Structure analysis of PCNA1 from Thermococcus kodakaraens... -

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Basic information

Entry
Database: PDB / ID: 3lx1
TitleCrystal Structure analysis of PCNA1 from Thermococcus kodakaraensis tk0535
ComponentsDNA polymerase sliding clamp 1
KeywordsDNA BINDING PROTEIN / PCNA / DNA processivity factor / trimer / toroidal / DNA replication / DNA-binding
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / 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 1
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3884
Polymers29,0991
Non-polymers2883
Water1,45981
1
A: DNA polymerase sliding clamp 1
hetero molecules

A: DNA polymerase sliding clamp 1
hetero molecules

A: DNA polymerase sliding clamp 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,16312
Polymers87,2983
Non-polymers8659
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area6170 Å2
ΔGint-138 kcal/mol
Surface area33160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.230, 89.230, 62.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 29099.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: pcn1, TK0535 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q5JF32
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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 14, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→29.21 Å / Num. obs: 19294 / % possible obs: 99.8 % / Redundancy: 5.57 % / Rmerge(I) obs: 0.094 / Χ2: 0.99 / Net I/σ(I): 7.9 / Scaling rejects: 812
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.075.430.5162.21052319201.2499.2
2.07-2.155.450.4552.51040318881.2199.5
2.15-2.255.510.38831067619231.1699.5
2.25-2.375.570.3423.41080719291.1299.8
2.37-2.525.520.28941066419161.0699.8
2.52-2.715.590.2314.6108141921199.9
2.71-2.995.590.1726.11090619370.94100
2.99-3.425.690.09410.61107319380.8100
3.42-4.35.730.05317.91115119390.799.9
4.3-29.215.580.0423.51118819830.6899.8

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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 reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.21 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.246 / WRfactor Rwork: 0.187 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.805 / SU B: 4.667 / SU ML: 0.131 / SU R Cruickshank DPI: 0.197 / SU Rfree: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.262 939 4.9 %RANDOM
Rwork0.199 ---
obs0.202 19035 98.55 %-
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: 71.82 Å2 / Biso mean: 33.664 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.36 Å20 Å2
2--0.72 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1956 0 15 81 2052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222143
X-RAY DIFFRACTIONr_angle_refined_deg1.7712.012905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78725.288104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76415420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6121515
X-RAY DIFFRACTIONr_chiral_restr0.1280.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211624
X-RAY DIFFRACTIONr_mcbond_it1.2021.51312
X-RAY DIFFRACTIONr_mcangle_it2.20722139
X-RAY DIFFRACTIONr_scbond_it3.4543831
X-RAY DIFFRACTIONr_scangle_it5.8144.5766
LS refinement shellResolution: 2→2.108 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 133 -
Rwork0.262 2589 -
all-2722 -
obs--97.08 %

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