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- PDB-2hii: heterotrimeric PCNA sliding clamp -

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Basic information

Entry
Database: PDB / ID: 2hii
Titleheterotrimeric PCNA sliding clamp
Components
  • PCNA1 (SSO0397)
  • PCNA2 (SSO1047)
  • PCNA3 (SSO0405)
KeywordsREPLICATION / sliding clamp / processivity factor / heterotrimeric / DNA replication
Function / homology
Function and homology information


leading strand elongation / DNA polymerase processivity factor activity / regulation of 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 1 / DNA polymerase sliding clamp 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsPascal, J.M. / Tsodikov, O.V. / Ellenberger, T.
CitationJournal: Mol.Cell / Year: 2006
Title: A Flexible Interface between DNA Ligase and PCNA Supports Conformational Switching and Efficient Ligation of DNA.
Authors: Pascal, J.M. / Tsodikov, O.V. / Hura, G.L. / Song, W. / Cotner, E.A. / Classen, S. / Tomkinson, A.E. / Tainer, J.A. / Ellenberger, T.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PCNA1 (SSO0397)
B: PCNA2 (SSO1047)
C: PCNA3 (SSO0405)
X: PCNA1 (SSO0397)
Y: PCNA2 (SSO1047)
Z: PCNA3 (SSO0405)


Theoretical massNumber of molelcules
Total (without water)170,9196
Polymers170,9196
Non-polymers00
Water0
1
A: PCNA1 (SSO0397)
B: PCNA2 (SSO1047)
C: PCNA3 (SSO0405)


Theoretical massNumber of molelcules
Total (without water)85,4593
Polymers85,4593
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-21 kcal/mol
Surface area33230 Å2
MethodPISA
2
X: PCNA1 (SSO0397)
Y: PCNA2 (SSO1047)
Z: PCNA3 (SSO0405)


Theoretical massNumber of molelcules
Total (without water)85,4593
Polymers85,4593
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-21 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.519, 87.179, 135.874
Angle α, β, γ (deg.)89.800, 86.360, 78.330
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21X
31A
41X
12B
22Y
32B
42Y
13C
23Z
33C
43Z

NCS domain segments:

Refine code: 3

Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEALAAA2 - 1172 - 117
211PHEALAXD2 - 1172 - 117
321PROLEUAA128 - 249128 - 249
421PROLEUXD128 - 249128 - 249
112MSELEUBB2 - 1141 - 113
212MSELEUYE2 - 1141 - 113
322VALARGBB125 - 244124 - 243
422VALARGYE125 - 244124 - 243
113MSEASNCC1 - 1131 - 113
213MSEASNZF1 - 1131 - 113
323ILELYSCC124 - 243124 - 243
423ILELYSZF124 - 243124 - 243

NCS ensembles :
ID
1
2
3

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Components

#1: Protein PCNA1 (SSO0397) / DNA polymerase sliding clamp B / Proliferating cell nuclear antigen homolog B / PCNA B


Mass: 29062.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnB, pcnA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P57766
#2: Protein PCNA2 (SSO1047) / DNA polymerase sliding clamp C / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27648.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnC, pcnA-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Z84
#3: Protein PCNA3 (SSO0405) / DNA polymerase sliding clamp A / Proliferating cell nuclear antigen homolog A / PCNA A


Mass: 28747.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pcnA, pcnA-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P57765

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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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 298 K / pH: 5.5
Details: 18-20% PEG 3350, 150mM ammonium citrate, 100mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 5.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 37657 / % possible obs: 93.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.3
Reflection shellResolution: 2.79→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.238 / % possible all: 68.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.876 / SU B: 44.611 / SU ML: 0.393 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1892 5 %RANDOM
Rwork0.215 ---
obs0.218 37555 92.8 %-
all-37555 --
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 mean: 32.63 Å2
Baniso -1Baniso -2Baniso -3
1-5.69 Å23 Å22.06 Å2
2---3.09 Å20.36 Å2
3----4.08 Å2
Refinement stepCycle: LAST / Resolution: 2.79→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11550 0 0 0 11550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.98115820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02951464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.42525.412510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.018152212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5011548
X-RAY DIFFRACTIONr_chiral_restr0.1030.21852
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028570
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2330.25058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.27968
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2408
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4761.57495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.635211886
X-RAY DIFFRACTIONr_scbond_it1.29134664
X-RAY DIFFRACTIONr_scangle_it1.9624.53934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A952tight positional0.040.05
2B932tight positional0.040.05
3C932tight positional0.040.05
1A887loose positional0.55
2B915loose positional0.395
3C913loose positional0.425
1A952tight thermal0.060.5
2B932tight thermal0.060.5
3C932tight thermal0.050.5
1A887loose thermal0.810
2B915loose thermal0.9510
3C913loose thermal0.8210
LS refinement shellResolution: 2.79→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 89 -
Rwork0.311 1739 -
obs--63.23 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.07050.2609-0.27064.96020.82292.33490.0279-0.03110.0093-0.0615-0.0267-0.0684-0.20330.2176-0.0012-0.208-0.0014-0.0476-0.08720.0126-0.157814.44239.1721-33.5781
21.3191.7194-1.36753.8146-1.47963.50240.0195-0.01050.15150.30540.04850.3758-0.39760.1405-0.0680.02840.0815-0.0078-0.0864-0.07570.00337.176353.61067.2267
31.68690.07130.26621.63722.03598.9134-0.02350.03840.10690.0439-0.00630.1380.189-0.16730.0298-0.3412-0.0319-0.0018-0.17980.0967-0.09930.938511.3706-3.5744
40.9268-0.4329-0.05274.18110.82193.13570.0016-0.0578-0.1126-0.17250.2151-0.02050.19690.0424-0.2167-0.1789-0.0498-0.0122-0.03190.0054-0.10668.7246-3.0334.4245
51.28780.5699-1.03292.4902-1.42944.049-0.02830.1217-0.08910.10520.0315-0.0878-0.12170.0878-0.0031-0.39490.0611-0.0407-0.1721-0.0101-0.1481.7198.976676.1464
61.6828-0.0984-0.10181.29961.90158.5024-0.07250.1147-0.0275-0.17280.07190.06940.3696-0.13430.0007-0.08220.01030.0019-0.19140.0634-0.0682-1.1029-33.052163.7351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2491 - 249
2X-RAY DIFFRACTION2BB2 - 2441 - 243
3X-RAY DIFFRACTION3CC1 - 2431 - 243
4X-RAY DIFFRACTION4XD1 - 2491 - 249
5X-RAY DIFFRACTION5YE2 - 2441 - 243
6X-RAY DIFFRACTION6ZF1 - 2431 - 243

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