[English] 日本語
Yorodumi
- PDB-4xkc: Crystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with M... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xkc
TitleCrystal Structure of GENOMES UNCOUPLED 4 (GUN4) in Complex with Magnesium Deuteroporphyrin IX
ComponentsYcf53-like protein
KeywordsLIGAND BINDING PROTEIN / Gun4 / Mg Deuteroporphyrin IX / Porphyrin-binding
Function / homology
Function and homology information


tetrapyrrole binding
Similarity search - Function
Gun4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #620 / GUN4, N-terminal ARM-like repeat domain / ARM-like repeat domain, GUN4-N terminal / GUN4-like / GUN4-like superfamily / GUN4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A ...Gun4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #620 / GUN4, N-terminal ARM-like repeat domain / ARM-like repeat domain, GUN4-N terminal / GUN4-like / GUN4-like superfamily / GUN4-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Arc Repressor Mutant, subunit A / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Magnesium deuteroporphyrin IX / Ycf53-like protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsChen, X. / Pu, H. / Liu, L.
CitationJournal: Mol Plant / Year: 2015
Title: Crystal Structures of GUN4 in Complex with Porphyrins.
Authors: Chen, X. / Pu, H. / Wang, X. / Long, W. / Lin, R. / Liu, L.
History
DepositionJan 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ycf53-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0242
Polymers26,4911
Non-polymers5331
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.849, 64.026, 106.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ycf53-like protein


Mass: 26490.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: sll0558 / Production host: Escherichia coli (E. coli) / References: UniProt: P72583
#2: Chemical ChemComp-MD9 / Magnesium deuteroporphyrin IX


Mass: 532.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H28MgN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: sodium cacodylate, sodium chloride, PEG 3350 / PH range: 6.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16064 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 18.7

-
Processing

Software
NameVersionClassification
HKL-2000refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
RefinementResolution: 2→32.013 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 799 5.11 %
Rwork0.1817 --
obs0.1841 15627 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 39 246 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081942
X-RAY DIFFRACTIONf_angle_d1.1912674
X-RAY DIFFRACTIONf_dihedral_angle_d13.744719
X-RAY DIFFRACTIONf_chiral_restr0.048280
X-RAY DIFFRACTIONf_plane_restr0.003340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.27871200.20412289X-RAY DIFFRACTION94
2.1253-2.28930.23821310.19062456X-RAY DIFFRACTION100
2.2893-2.51970.23541440.18152456X-RAY DIFFRACTION100
2.5197-2.8840.25651250.19492482X-RAY DIFFRACTION100
2.884-3.63280.22891260.18422517X-RAY DIFFRACTION100
3.6328-32.01710.20231530.16592628X-RAY DIFFRACTION100

+
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://pdbjlvh1.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