4YTE

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.256
R-Value Work: 0.226
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

N-terminal domain of HmdIII from Methanocaldococcus jannaschii

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

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58125
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.256
R-Value Work: 0.226
R-Value Observed: 0.227
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-23

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2016-03-23
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.