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- PDB-1rwz: Crystal Structure of Proliferating Cell Nuclear Antigen (PCNA) fr... -

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Basic information

Entry
Database: PDB / ID: 1rwz
TitleCrystal Structure of Proliferating Cell Nuclear Antigen (PCNA) from A. fulgidus
ComponentsDNA polymerase sliding clamp
KeywordsREPLICATION / sliding clamp / torus / processivity factor
Function / homology
Function and homology information


DNA polymerase processivity factor activity / leading strand elongation / 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
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair
Authors: Chapados, B.R. / Hosfield, D.J. / Han, S. / Qiu, J. / Yelent, B. / Shen, B. / Tainer, J.A.
History
DepositionDec 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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
A: DNA polymerase sliding clamp


Theoretical massNumber of molelcules
Total (without water)27,3021
Polymers27,3021
Non-polymers00
Water5,693316
1
A: DNA polymerase sliding clamp

A: DNA polymerase sliding clamp

A: DNA polymerase sliding clamp


Theoretical massNumber of molelcules
Total (without water)81,9053
Polymers81,9053
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
2
A: DNA polymerase sliding clamp
x 12


Theoretical massNumber of molelcules
Total (without water)327,61812
Polymers327,61812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation82_555-y,z,-x1
Buried area22690 Å2
ΔGint-126 kcal/mol
Surface area116990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)244.355, 244.355, 244.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-1021-

HOH

21A-1082-

HOH

31A-1149-

HOH

41A-1201-

HOH

51A-1294-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by applying the transformation matrix: [0 1 0] [0 0 1] [1 0 0] and [0 0 1] [1 0 0] [0 1 0]

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Components

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


Mass: 27301.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: PCN, AF0335 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29912
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Na/K phosphate, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMTris1droppH8.0
3250 mM1dropNaCl
41.4-1.6 Msodium/pootassium phosphate1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.2398 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 16, 2000
RadiationMonochromator: triangle Ge(111), conical Si/Rh mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 56483 / Num. obs: 56483 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 93.9 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 5.8 / Num. unique all: 5493 / Rsym value: 0.263 / % possible all: 96.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model built from 2.1 angstrom resolution data phased by a single anomalous derivative (ethyl mercury phosphate)

Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.238 5563 random
Rwork0.219 --
all0.221 55307 -
obs0.221 55307 -
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 0 316 2222
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d1.3
X-RAY DIFFRACTIONx_torsion_deg25.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.66
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.3

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