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- PDB-4cs5: Crystal Structure of PCNA from Litopenaeus vannamei -

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Basic information

Entry
Database: PDB / ID: 4cs5
TitleCrystal Structure of PCNA from Litopenaeus vannamei
ComponentsPROLIFERATING CELL NUCLEAR ANTIGEN
KeywordsNUCLEAR PROTEIN / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding / nucleus
Similarity search - Function
Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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 ...Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / 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
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesLITOPENAEUS VANNAMEI (Pacific white shrimp)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCarrasco-Miranda, J.S. / Lopez-Zavala, A.A. / De-La-Mora, E. / Rudino-Pinera, E. / Brieba, L.G. / Sotelo-Mundo, R.R.
Citation
Journal: Plos One / Year: 2014
Title: Crystal Structure of the Shrimp Proliferating Cell Nuclear Antigen: Structural Complementarity with Wssv DNA Polymerase Pip-Box.
Authors: Carrasco-Miranda, J.S. / Lopez-Zavala, A.A. / Arvizu-Flores, A.A. / Garcia-Orozco, K.D. / Stojanoff, V. / Rudino-Pinera, E. / Brieba, L.G. / Sotelo-Mundo, R.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and X-Ray Diffraction Studies of Crustacean Proliferating Cell Nuclear Antigen.
Authors: Carrasco-Miranda, J.S. / Cardona-Felix, C.S. / Lopez-Zavala, A.A. / De-La-Re-Vega, E. / De La Mora, E. / Rudino-Pinera, E. / Sotelo-Mundo, R.R. / Brieba, L.G.
History
DepositionMar 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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: PROLIFERATING CELL NUCLEAR ANTIGEN
B: PROLIFERATING CELL NUCLEAR ANTIGEN
C: PROLIFERATING CELL NUCLEAR ANTIGEN


Theoretical massNumber of molelcules
Total (without water)86,5203
Polymers86,5203
Non-polymers00
Water0
1
A: PROLIFERATING CELL NUCLEAR ANTIGEN


Theoretical massNumber of molelcules
Total (without water)28,8401
Polymers28,8401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROLIFERATING CELL NUCLEAR ANTIGEN


Theoretical massNumber of molelcules
Total (without water)28,8401
Polymers28,8401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROLIFERATING CELL NUCLEAR ANTIGEN


Theoretical massNumber of molelcules
Total (without water)28,8401
Polymers28,8401
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)144.570, 83.380, 74.310
Angle α, β, γ (deg.)90.00, 117.65, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 1:254 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
211CHAIN B AND (RESSEQ 1:254 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)
311CHAIN C AND (RESSEQ 1:254 ) AND (NOT ELEMENT H) AND (NOT ELEMENT D)

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Components

#1: Protein PROLIFERATING CELL NUCLEAR ANTIGEN /


Mass: 28840.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LITOPENAEUS VANNAMEI (Pacific white shrimp)
Plasmid: PJ404 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): SI / References: UniProt: G1E6N7
Sequence detailsTHE AMINOACID SEQUENCE OF THE PDB FILE LACK THE LAST 6 C- TERMINAL RESIDUES COMPARED TO THE ...THE AMINOACID SEQUENCE OF THE PDB FILE LACK THE LAST 6 C- TERMINAL RESIDUES COMPARED TO THE SEQUENCE REPORTED IN UNIPROT. THIS IS BECAUSE THERE IS NO ELECTRONIC DENSITY TO INCLUDE THAT RESIDUES IN THE MODEL.

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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: 2.36 Å3/Da / Density % sol: 47.35 %
Crystal growpH: 7.5
Details: 300 MM CACL2, 100 MM SODIUM HEPES PH 7.5 AND 30%(V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Mar 31, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 14802 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 2.96 % / Biso Wilson estimate: 55.53 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.69
Reflection shellResolution: 3→3.1 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.57 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL OF LVPCNA BASED ON PDB ENTRY 1VYM

1vym


Resolution: 3→28.058 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 35.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3108 736 5 %
Rwork0.2648 --
obs0.2672 14782 93.71 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.628 Å2 / ksol: 0.275 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--22.7877 Å20 Å2-8.267 Å2
2---24.6962 Å20 Å2
3---44.0041 Å2
Refinement stepCycle: LAST / Resolution: 3→28.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5877 0 0 0 5877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015963
X-RAY DIFFRACTIONf_angle_d1.4898049
X-RAY DIFFRACTIONf_dihedral_angle_d18.1462241
X-RAY DIFFRACTIONf_chiral_restr0.116941
X-RAY DIFFRACTIONf_plane_restr0.0061035
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1953X-RAY DIFFRACTIONPOSITIONAL
12B1953X-RAY DIFFRACTIONPOSITIONAL0.047
13C1948X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.23150.41181390.37082893X-RAY DIFFRACTION97
3.2315-3.55610.34641440.29292827X-RAY DIFFRACTION95
3.5561-4.06940.40931360.32112668X-RAY DIFFRACTION90
4.0694-5.12190.26851450.22112825X-RAY DIFFRACTION94
5.1219-28.05880.24131720.21442833X-RAY DIFFRACTION93

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