6J0J | pdb_00006j0j

Crystal structure of Proliferating Cell Nuclear Antigen from Leishmania donovani with an unexplained density near residues Pro229,Pr0267 and Ala285

PDB DOI: https://doi.org/10.2210/pdb6J0J/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Leishmania donovani
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-24 Released: 2019-01-23
Deposition Author(s): Iqbal, N., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.223 (Depositor), 0.226 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Proliferating Cell Nuclear Antigen from Leishmania donovani with an unexplained density near residues Pro229,Pr0267 and Ala285

Iqbal, N., Sharma, S., Singh, T.P.

To be published.

Macromolecule Content

Total Structure Weight: 199.19 kDa
Atom Count: 11,713
Modeled Residue Count: 1,501
Deposited Residue Count: 1,812
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A B [auth D] C [auth E] D [auth B] E [auth C] A, B [auth D], C [auth E], D [auth B], E [auth C], F	302	Leishmania donovani	Mutation(s): 0 Gene Names: PCNA
UniProt
Find proteins for B5TV91 (Leishmania donovani) Explore B5TV91 Go to UniProtKB: B5TV91
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5TV91
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth E] MOL2 format, chain H [auth E] mmCIF format, chain H [auth E]	H [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.223 (Depositor), 0.226 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.46	α = 90
b = 150.91	β = 90
c = 170.57	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.