6H1W | pdb_00006h1w

Crystal Structure of protein MJ1004 from Mathanocaldococcus jannaschii

PDB DOI: https://doi.org/10.2210/pdb6H1W/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-12 Released: 2019-07-31
Deposition Author(s): Alfonso Martinez-Cruz, L., Oyenarte, I., Fernandez-Rodriguez, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of protein MJ1004 from Mathanocaldococcus jannaschii

Alfonso Martinez-Cruz, L., Oyenarte, I., Fernandez-Rodriguez, C.

To be published.

Macromolecule Content

Total Structure Weight: 49.91 kDa
Atom Count: 3,284
Modeled Residue Count: 415
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MJ1004	A, B	214	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: MJ1004
UniProt
Find proteins for Q58410 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58410 Go to UniProtKB: Q58410
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58410
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.899	α = 90
b = 80.899	β = 90
c = 178.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2019-07-31

Deposition Author(s):

Alfonso Martinez-Cruz, L.

Fernandez-Rodriguez, C.

Funding Organization	Location	Grant Number
	Spain	PI2010-17
	Spain	ETORTEK IE05-147, IE07-202
	Spain	Exp. 7/13/08/2006/11
	Spain	Exp. 7/13/08/2005/14
	Spain	MICINN BFU2010-17857
	Spain	CSD2008-00005

Revision History (Full details and data files)

Version 1.0: 2019-07-31
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.