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- PDB-5a6d: Proliferating Cell Nuclear Antigen, PCNA, from Thermococcus gamma... -

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Basic information

Entry
Database: PDB / ID: 5a6d
TitleProliferating Cell Nuclear Antigen, PCNA, from Thermococcus gammatolerans
ComponentsDNA POLYMERASE SLIDING CLAMP
KeywordsDNA BINDING PROTEIN / NUCLEAR PROTEIN / PCNA / THERMOCOCCUS / GAMMATOLERANS / PROLIFERATING / NUCLEAR ANTIGEN.
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / 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
Similarity search - Component
Biological speciesTHERMOCOCCUS GAMMATOLERANS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVenancio-Landeros, A. / Cardona-Felix, C.S. / Rudino-Pinera, E.
CitationJournal: Biochem Biophys Rep / Year: 2016
Title: Cloning, recombinant production and crystallographic structure of Proliferating Cell Nuclear Antigen from radioresistant archaeon Thermococcus gammatolerans.
Authors: Venancio-Landeros, A.A. / Rudino-Pinera, E. / Cardona-Felix, C.S.
History
DepositionJun 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA POLYMERASE SLIDING CLAMP
B: DNA POLYMERASE SLIDING CLAMP


Theoretical massNumber of molelcules
Total (without water)56,3122
Polymers56,3122
Non-polymers00
Water00
1
B: DNA POLYMERASE SLIDING CLAMP

B: DNA POLYMERASE SLIDING CLAMP

B: DNA POLYMERASE SLIDING CLAMP


Theoretical massNumber of molelcules
Total (without water)84,4693
Polymers84,4693
Non-polymers00
Water0
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 area4110 Å2
ΔGint-19.5 kcal/mol
Surface area33580 Å2
MethodPISA
2
A: DNA POLYMERASE SLIDING CLAMP

A: DNA POLYMERASE SLIDING CLAMP

A: DNA POLYMERASE SLIDING CLAMP


Theoretical massNumber of molelcules
Total (without water)84,4693
Polymers84,4693
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area4250 Å2
ΔGint-12.1 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.669, 92.669, 63.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein DNA POLYMERASE SLIDING CLAMP / PROLIFERATING CELL NUCLEAR ANTIGEN HOMOLOG / PCNA / PROLIFERA TING CELL NUCLEAR ANTIGEN


Mass: 28156.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS GAMMATOLERANS (archaea) / Strain: EJ3 / Plasmid: PCOLD I / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: C5A5N6
Sequence detailsTHE FIRTS M AND THE LAST TWO E PROTEIN RESIDUES PRESENT IN THE UNIPROT SEQUENCE ARE NOT VISIBLE IN ...THE FIRTS M AND THE LAST TWO E PROTEIN RESIDUES PRESENT IN THE UNIPROT SEQUENCE ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP OF THIS DEPOSIT

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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: 3.24 Å3/Da / Density % sol: 62.01 % / Description: NONE
Crystal growpH: 5.2
Details: 100 MM CITRATE BUFFER PH 5.2 2.8 M AMMONIUM SULPHATE 7.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.18076
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 2015
Details: FLAT COLLIMATING RH COATED MIRROR, TOROIDAL FOCUSSING MIRROR
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 15022 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 68.43 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LX1

3lx1


Resolution: 2.8→49.861 Å / SU ML: 0.37 / σ(F): 1.97 / Phase error: 25.48 / Stereochemistry target values: ML / Details: REFINEMENT WAS PERFORMED USING RESTRAINED NCS
RfactorNum. reflection% reflection
Rfree0.2379 755 5 %
Rwork0.1883 --
obs0.1908 15012 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.16 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 0 0 3898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113950
X-RAY DIFFRACTIONf_angle_d1.5085318
X-RAY DIFFRACTIONf_dihedral_angle_d15.0271522
X-RAY DIFFRACTIONf_chiral_restr0.054622
X-RAY DIFFRACTIONf_plane_restr0.008684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-3.01630.34531700.24452859X-RAY DIFFRACTION100
3.0163-3.31980.33051500.22562858X-RAY DIFFRACTION100
3.3198-3.80.26261600.19692806X-RAY DIFFRACTION100
3.8-4.7870.21761300.16562866X-RAY DIFFRACTION99
4.787-49.86870.19141450.18042868X-RAY DIFFRACTION100

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