[English] 日本語
Yorodumi
- PDB-5zkh: Crystal Structure of N-terminal Domain of Plasmodium falciparum p43 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zkh
TitleCrystal Structure of N-terminal Domain of Plasmodium falciparum p43
ComponentsAminoacyl tRNA synthetase complex-interacting multifunctional protein P43
KeywordsLIGASE / GST-like domain / AIMP1 / Plasmodium
Function / homologytRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Glutathione S-transferase, C-terminal domain superfamily / tRNA binding / Nucleic acid-binding, OB-fold / tRNA-binding domain-containing protein
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.991 Å
AuthorsManickam, Y. / Sharma, A. / Khan, S.
CitationJournal: To Be Published
Title: Structural analysis of aminoacyl-tRNA synthetase-interacting multifunctional proteins from plasmodium species
Authors: Manickam, Y. / Sharma, A.
History
DepositionMar 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminoacyl tRNA synthetase complex-interacting multifunctional protein P43
B: Aminoacyl tRNA synthetase complex-interacting multifunctional protein P43


Theoretical massNumber of molelcules
Total (without water)42,7942
Polymers42,7942
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-13 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.710, 44.371, 77.472
Angle α, β, γ (deg.)90.000, 111.940, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Aminoacyl tRNA synthetase complex-interacting multifunctional protein P43


Mass: 21396.859 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate Dd2) (eukaryote)
Gene: PFDG_03875 / Plasmid: pETM-11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0L7M8L6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7156 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.081 / Χ2: 1.348 / Net I/σ(I): 10.5 / Num. measured all: 43159
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
3-3.055.30.5523371.455198.8
3.05-3.115.50.513621.363199.7
3.11-3.175.70.4643521.351199.4
3.17-3.235.80.4263481.334199.4
3.23-3.360.3813671.2681100
3.3-3.3860.2863351.312199.4
3.38-3.466.10.2313771.324199.7
3.46-3.566.30.1863261.2671100
3.56-3.666.20.163651.2441100
3.66-3.786.30.1443621.3021100
3.78-3.916.20.1133581.3371100
3.91-4.076.30.0933521.3651100
4.07-4.266.20.083551.3371100
4.26-4.486.30.0633601.3931100
4.48-4.766.20.0613521.3481100
4.76-5.136.20.0543581.3571100
5.13-5.646.20.0633741.3981100
5.64-6.466.10.0613611.2811100
6.46-8.136.10.0443641.3191100
8.13-505.70.0313911.6171100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.991→36.464 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 335 4.69 %
Rwork0.2142 --
obs0.2161 7144 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.46 Å2 / Biso mean: 72.5903 Å2 / Biso min: 32.48 Å2
Refinement stepCycle: final / Resolution: 2.991→36.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2499 0 0 0 2499
Num. residues----328
Refinement TLS params.Method: refined / Origin x: -9.5789 Å / Origin y: 3.7971 Å / Origin z: 17.2137 Å
111213212223313233
T0.4723 Å2-0.0116 Å20.0216 Å2-0.3832 Å2-0.0362 Å2--0.3779 Å2
L3.5341 °20.7848 °2-0.6255 °2-2.4033 °2-0.1102 °2--2.1418 °2
S0.0025 Å °0.007 Å °-0.0754 Å °0.0836 Å °-0.0036 Å °0.2449 Å °-0.0512 Å °-0.0276 Å °0.0428 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 171
2X-RAY DIFFRACTION1allB2 - 171

+
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