3BJO

Crystal structure of the C-terminal domain of a possible ATP-binding protein from Methanocaldococcus jannaschii DSM 2661

PDB DOI: https://doi.org/10.2210/pdb3BJO/pdb

Classification: NUCLEOTIDE BINDING PROTEIN
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2007-12-04 Released: 2007-12-18
Deposition Author(s): Tan, K., Hatzos, C., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.217
R-Value Work: 0.203
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

The structure of the C-terminal domain of a possible ATP-binding protein from Methanocaldococcus jannaschii DSM 2661.

Tan, K., Hatzos, C., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 12.22 kDa
Atom Count: 916
Modelled Residue Count: 103
Deposited Residue Count: 103
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized ATP-binding protein MJ1010	A	103	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0 Gene Names: MJ1010
UniProt
Find proteins for Q58416 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58416 Go to UniProtKB: Q58416
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q58416
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.217
R-Value Work: 0.203
R-Value Observed: 0.203
Space Group: F 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.472	α = 90
b = 83.264	β = 90
c = 125.641	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXS	phasing
MLPHARE	phasing
DM	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-12-18

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-12-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance

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.