4YTE | pdb_00004yte

N-terminal domain of HmdIII from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb4YTE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-17 Released: 2016-03-23 
• Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.
• Funding Organization(s): JST-PRESTO, Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: other

Literature

N-terminal domain of HmdIII from Methanocaldococcus jannaschii

Fujishiro, T., Kahnt, J., Ermler, U., Shima, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.22 kDa 
• Atom Count: 1,560 
• Modeled Residue Count: 194 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ0715	A	194	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: MJ0715
UniProt
Find proteins for Q58125 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58125  Go to UniProtKB:  Q58125

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.78	α = 90
b = 53.78	β = 90
c = 127.27	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Fujishiro, T., Ermler, U., Shima, S.

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Funding Organization	Location	Grant Number
JST-PRESTO	Japan	--
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Refinement description