[English] 日本語
Yorodumi
- PDB-8gj5: fungal pcna and peptidomimetic -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gj5
Titlefungal pcna and peptidomimetic
Components
  • Proliferating cell nuclear antigen
  • THR-ASP-ILE-ARG-ASN-PHE-PHE-HIS-SER
KeywordsREPLICATION / PCNA / proliferating cell nuclear antigen / replication protein
Function / homology
Function and homology information


myosin binding / DNA polymerase processivity factor activity / regulation of DNA replication / DNA replication / DNA binding / membrane / nucleus
Similarity search - Function
Myosin-binding domain / Mysoin-binding motif of peroxisomes / 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 / :
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVandborg, B. / Bruning, J.B.
Funding support Australia, 1items
OrganizationGrant numberCountry
Not funded Australia
CitationJournal: J Fungi / Year: 2023
Title: Towards a High-Affinity Peptidomimetic Targeting Proliferating Cell Nuclear Antigen from Aspergillus fumigatus.
Authors: Vandborg, B.C. / Horsfall, A.J. / Pederick, J.L. / Abell, A.D. / Bruning, J.B.
History
DepositionMar 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: THR-ASP-ILE-ARG-ASN-PHE-PHE-HIS-SER
E: THR-ASP-ILE-ARG-ASN-PHE-PHE-HIS-SER
F: THR-ASP-ILE-ARG-ASN-PHE-PHE-HIS-SER


Theoretical massNumber of molelcules
Total (without water)90,9536
Polymers90,9536
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-46 kcal/mol
Surface area34410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.929, 96.976, 108.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Proliferating cell nuclear antigen


Mass: 28221.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: CDV57_03149 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A229Y5V5
#2: Protein/peptide THR-ASP-ILE-ARG-ASN-PHE-PHE-HIS-SER


Mass: 2096.485 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M Tacsimate pH 4.0 0.1M Na Acetate, 16% PEG 3350 tray

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.49 Å / Num. obs: 39804 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.028 / Rrim(I) all: 0.104 / Χ2: 1.02 / Net I/σ(I): 20.1 / Num. measured all: 540450
Reflection shellResolution: 2.3→2.39 Å / % possible obs: 99.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 2.017 / Num. measured all: 51539 / Num. unique obs: 4085 / CC1/2: 0.616 / Rpim(I) all: 0.58 / Rrim(I) all: 2.101 / Χ2: 1.02 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→47.2 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 2021 5.09 %
Rwork0.239 --
obs0.2396 39732 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5873 0 0 144 6017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045952
X-RAY DIFFRACTIONf_angle_d0.9228091
X-RAY DIFFRACTIONf_dihedral_angle_d16.158834
X-RAY DIFFRACTIONf_chiral_restr0.057998
X-RAY DIFFRACTIONf_plane_restr0.0061045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.38621360.35862614X-RAY DIFFRACTION99
2.36-2.420.32331450.32642676X-RAY DIFFRACTION100
2.42-2.490.30951540.30612636X-RAY DIFFRACTION100
2.49-2.570.33961280.31552670X-RAY DIFFRACTION100
2.57-2.670.37781600.31172646X-RAY DIFFRACTION100
2.67-2.770.31041680.3112666X-RAY DIFFRACTION100
2.77-2.90.29741440.2922672X-RAY DIFFRACTION100
2.9-3.050.30621380.28012681X-RAY DIFFRACTION100
3.05-3.240.25531290.26492687X-RAY DIFFRACTION100
3.24-3.490.25181480.24532703X-RAY DIFFRACTION100
3.49-3.840.23261250.22532713X-RAY DIFFRACTION100
3.84-4.40.21261480.20462743X-RAY DIFFRACTION100
4.4-5.540.22731630.18562727X-RAY DIFFRACTION100
5.54-47.20.20521350.22052877X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.523 Å / Origin y: 17.1581 Å / Origin z: 19.5856 Å
111213212223313233
T0.4295 Å20.0248 Å20.0278 Å2-0.2571 Å20.1084 Å2--0.3589 Å2
L0.9944 °2-0.1034 °2-0.2749 °2-0.5395 °20.6003 °2--1.0022 °2
S0.0962 Å °0.03 Å °0.0703 Å °-0.0359 Å °-0.0145 Å °-0.0296 Å °-0.096 Å °-0.0435 Å °-0.0713 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more