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- PDB-6k2m: Crystal structure of the complex of Proliferating Cell Nuclear An... -

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Basic information

Entry
Database: PDB / ID: 6k2m
TitleCrystal structure of the complex of Proliferating Cell Nuclear Antigen from Leishmania donovani with arginine at 3.19 A resolution.
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


PCNA complex / 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
ARGININE / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsViswanathan, V. / Iqbal, N. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of the complex of Proliferating Cell Nuclear Antigen from Leishmania donovani with arginine at 3.19 A resolution.
Authors: Viswanathan, V. / Iqbal, N. / Sharma, S. / Singh, T.P.
History
DepositionMay 15, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,3438
Polymers198,9936
Non-polymers3502
Water1,31573
1
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6724
Polymers99,4963
Non-polymers1751
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-14 kcal/mol
Surface area32960 Å2
MethodPISA
2
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6724
Polymers99,4963
Non-polymers1751
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-13 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.926, 150.588, 171.009
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Proliferating cell nuclear antigen


Mass: 33165.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: PCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B5TV91
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4.4 Å3/Da / Density % sol: 76.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 3.19→106.63 Å / Num. obs: 58894 / % possible obs: 99.38 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.028 / Rrim(I) all: 0.06 / Net I/σ(I): 16.3
Reflection shellResolution: 3.19→3.24 Å / Redundancy: 5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2924 / CC1/2: 0.752 / Rpim(I) all: 0.323 / Rrim(I) all: 0.732 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J0J

6j0j


Resolution: 3.19→106.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 16.979 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R: 0.617 / ESU R Free: 0.338
RfactorNum. reflection% reflectionSelection details
Rfree0.22695 3020 5.1 %RANDOM
Rwork0.16694 ---
obs0.17011 55874 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 110.526 Å2
Baniso -1Baniso -2Baniso -3
1-4.94 Å20 Å20 Å2
2--0.1 Å2-0 Å2
3----5.04 Å2
Refinement stepCycle: 1 / Resolution: 3.19→106.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11605 0 24 73 11702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311797
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711083
X-RAY DIFFRACTIONr_angle_refined_deg1.7271.63215914
X-RAY DIFFRACTIONr_angle_other_deg1.2291.57725737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.16951489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40323.247579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.143152137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1661563
X-RAY DIFFRACTIONr_chiral_restr0.0690.21543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.27811.3745998
X-RAY DIFFRACTIONr_mcbond_other10.27611.3735997
X-RAY DIFFRACTIONr_mcangle_it14.78317.0347473
X-RAY DIFFRACTIONr_mcangle_other14.78217.0347474
X-RAY DIFFRACTIONr_scbond_it11.58612.4715799
X-RAY DIFFRACTIONr_scbond_other11.58512.475799
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other17.33618.2498441
X-RAY DIFFRACTIONr_long_range_B_refined20.60112483
X-RAY DIFFRACTIONr_long_range_B_other20.612484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.188→3.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 208 -
Rwork0.331 4114 -
obs--99.72 %

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