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- PDB-7wp3: Crystal structure of the complex of proliferating cell nuclear an... -

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Basic information

Entry
Database: PDB / ID: 7wp3
TitleCrystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / PCNA / PCNA-PNT Complex / Leishmania donovani
Function / homology
Function and homology information


DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding / nucleus
Similarity search - Function
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 / :
Similarity search - Domain/homology
1,5-BIS(4-AMIDINOPHENOXY)PENTANE / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.954 Å
AuthorsAhmad, M.I. / Yadav, S.P. / Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/2020/July/86 India
CitationJournal: To Be Published
Title: Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution
Authors: Ahmad, M.I. / Yadav, S.P. / Singh, P.K. / Sharma, P. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionJan 22, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 15, 2022ID: 5B7O
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)191,9018
Polymers191,2206
Non-polymers6812
Water1,15364
1
A: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9514
Polymers95,6103
Non-polymers3401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-13 kcal/mol
Surface area32850 Å2
MethodPISA
2
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9514
Polymers95,6103
Non-polymers3401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-14 kcal/mol
Surface area33650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.024, 150.664, 170.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Proliferating cell nuclear antigen


Mass: 31870.076 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 (E. coli) / References: UniProt: B5TV91
#2: Chemical ChemComp-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, Antimicrobial*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.38 Å3/Da / Density % sol: 71.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 20% PEG 3350, 200mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2015
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.95→43.49 Å / Num. obs: 72691 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rsym value: 0.12 / Net I/σ(I): 11.6
Reflection shellResolution: 2.95→3.03 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1 / Num. unique obs: 4451 / % possible all: 84.52

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B7O

5b7o
PDB Unreleased entry


Resolution: 2.954→43.485 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: FREE R-VALUE / ESU R: 0.432 / ESU R Free: 0.31
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2567 1437 1.977 %
Rwork0.211 71254 -
all0.212 --
obs-72691 98.807 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 90.593 Å2
Baniso -1Baniso -2Baniso -3
1-0.136 Å20 Å20 Å2
2--0.044 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.954→43.485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11514 0 50 64 11628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311734
X-RAY DIFFRACTIONr_bond_other_d0.0350.01511232
X-RAY DIFFRACTIONr_angle_refined_deg1.311.63215828
X-RAY DIFFRACTIONr_angle_other_deg2.2911.5825902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86451476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.7623.368570
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.815104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.375152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3421560
X-RAY DIFFRACTIONr_chiral_restr0.050.21530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213198
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022570
X-RAY DIFFRACTIONr_nbd_refined0.2180.22401
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2310.210927
X-RAY DIFFRACTIONr_nbtor_refined0.1650.25791
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.25146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2334
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0780.215
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4680.218
X-RAY DIFFRACTIONr_nbd_other0.5050.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3590.24
X-RAY DIFFRACTIONr_mcbond_it7.4249.0715940
X-RAY DIFFRACTIONr_mcbond_other7.4259.0695939
X-RAY DIFFRACTIONr_mcangle_it11.06213.6057404
X-RAY DIFFRACTIONr_mcangle_other11.06213.6077405
X-RAY DIFFRACTIONr_scbond_it9.33610.175794
X-RAY DIFFRACTIONr_scbond_other9.3310.1685792
X-RAY DIFFRACTIONr_scangle_it14.27414.8428424
X-RAY DIFFRACTIONr_scangle_other14.27414.8428424
X-RAY DIFFRACTIONr_lrange_it19.41175.60147001
X-RAY DIFFRACTIONr_lrange_other19.41175.646998
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.954-3.030.371980.40444260.40353570.4720.43984.45020.405
3.03-3.1130.3911000.38851200.38852300.5260.52999.80880.391
3.113-3.2030.342860.35749900.35750770.6610.66699.98030.354
3.203-3.3010.3541070.32548510.32549580.7080.7391000.314
3.301-3.4080.371030.29446470.29547500.7580.7891000.275
3.408-3.5270.314870.26845540.26946410.8350.8391000.246
3.527-3.6590.288920.25643850.25744770.8720.891000.233
3.659-3.8080.307760.22542530.22643290.8710.9131000.2
3.808-3.9750.25820.20240760.20341580.9230.9271000.175
3.975-4.1680.252780.18638840.18739620.910.9351000.154
4.168-4.3910.257830.16937060.17137890.9140.9481000.141
4.391-4.6540.214750.1435230.14235980.9440.9641000.12
4.654-4.9720.161590.1433220.14133810.9620.9631000.123
4.972-5.3640.209470.15431100.15431570.9480.9561000.134
5.364-5.8670.245690.18428780.18629470.9290.9441000.16
5.867-6.5450.273620.21926080.22126700.9330.9241000.195
6.545-7.5290.269490.20323290.20523780.9160.9361000.183
7.529-9.1530.171410.15219900.15220310.9630.9651000.152
9.153-12.6660.203270.15716020.15816290.9570.9671000.166
12.666-43.4850.269160.29810000.29710200.950.92799.60780.32

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