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- PDB-2nti: Crystal structure of PCNA123 heterotrimer. -

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Basic information

Entry
Database: PDB / ID: 2nti
TitleCrystal structure of PCNA123 heterotrimer.
Components(DNA polymerase sliding clamp ...) x 3
KeywordsDNA BINDING PROTEIN / protein-protein interaction / PCNA123 heterotrimer / PCNA12 heterodimer
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
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL / BROMIDE ION / : / 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: 2.5 Å
AuthorsHlinkova, V. / Ling, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of monomeric, dimeric and trimeric PCNA: PCNA-ring assembly and opening.
Authors: Hlinkova, V. / Xing, G. / Bauer, J. / Shin, Y.J. / Dionne, I. / Rajashankar, K.R. / Bell, S.D. / Ling, H.
History
DepositionNov 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: DNA polymerase sliding clamp B
E: DNA polymerase sliding clamp C
F: DNA polymerase sliding clamp A
A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
C: DNA polymerase sliding clamp A
G: DNA polymerase sliding clamp B
H: DNA polymerase sliding clamp C
I: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)252,54865
Polymers247,8099
Non-polymers4,73856
Water18,8441046
1
D: DNA polymerase sliding clamp B
E: DNA polymerase sliding clamp C
F: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,52127
Polymers82,6033
Non-polymers1,91824
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-28 kcal/mol
Surface area32190 Å2
MethodPISA, PQS
2
A: DNA polymerase sliding clamp B
B: DNA polymerase sliding clamp C
C: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96120
Polymers82,6033
Non-polymers1,35817
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-21 kcal/mol
Surface area32480 Å2
MethodPISA, PQS
3
G: DNA polymerase sliding clamp B
H: DNA polymerase sliding clamp C
I: DNA polymerase sliding clamp A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,06518
Polymers82,6033
Non-polymers1,46215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-21 kcal/mol
Surface area32530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)148.140, 222.330, 80.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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DNA polymerase sliding clamp ... , 3 types, 9 molecules DAGEBHFCI

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


Mass: 27521.695 Da / Num. of mol.: 3 / Mutation: F2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnB, pcnA-2 / Plasmid: pET33b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: P57766
#2: Protein DNA polymerase sliding clamp C / Proliferating cell nuclear antigen homolog C / PCNA C


Mass: 27592.279 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnC, pcnA-2 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: Q97Z84
#3: Protein DNA polymerase sliding clamp A / Proliferating cell nuclear antigen homolog A / PCNA A


Mass: 27489.119 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: pcnA, pcnA-1 / Plasmid: pET30a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL 21 (DE3) / References: UniProt: P57765

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Non-polymers , 4 types, 1102 molecules

#4: Chemical...
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-7PG / 2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL


Mass: 384.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H36O9
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5 M NH4(SO4)2, 0.1 M Tris 7.5, 2% Peg400, 1.6% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 88416 / Num. obs: 88416 / % possible obs: 95.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.739
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 1.8 / % possible all: 93.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PCNA1, PCNA2 and PCNA3 from Sulfolobus solfataricus

Resolution: 2.5→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2505 1796 -Random
Rwork0.2139 ---
all0.2113 88416 --
obs0.2113 88416 95.7 %-
Displacement parametersBiso mean: 31.0928 Å2
Baniso -1Baniso -2Baniso -3
1--0.733 Å20 Å20 Å2
2---3.966 Å20 Å2
3---4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.289 Å0.641 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17361 0 81 1046 18488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.009147
X-RAY DIFFRACTIONr_mcbond_it1.227
X-RAY DIFFRACTIONr_angle_refined_deg1.15475
X-RAY DIFFRACTIONr_gen_planes_refined0.003
X-RAY DIFFRACTIONr_chiral_restr0.08
LS refinement shellResolution: 2.5→2.61 Å /
Rfactor% reflection
Rfree0.324 -
Rwork0.288 -
obs-93.6 %

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