3CET

Crystal structure of the pantheonate kinase-like protein Q6M145 at the resolution 1.8 A. Northeast Structural Genomics Consortium target MrR63

PDB DOI: https://doi.org/10.2210/pdb3CET/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Methanococcus maripaludis S2
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-02-29 Released: 2008-03-18
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, J.F., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.246
R-Value Work: 0.219
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of the pantheonate kinase-like protein Q6M145 at the resolution 1.8 A. Northeast Structural Genomics Consortium target MrR63.

Kuzin, A.P., Su, M., Seetharaman, J., Forouhar, F., Wang, D., Fang, Y., Cunningham, K., Ma, L.-C., Xiao, R., Liu, J., Baran, J.F., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 74.6 kDa
Atom Count: 5,178
Modelled Residue Count: 630
Deposited Residue Count: 668
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Conserved archaeal protein	A, B	334	Methanococcus maripaludis S2	Mutation(s): 13 Gene Names: MMP0072
UniProt
Find proteins for Q6M145 (Methanococcus maripaludis (strain S2 / LL)) Explore Q6M145 Go to UniProtKB: Q6M145
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6M145
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth B] MOL2 format, chain C [auth B] MOL2 format, chain D [auth B]	C [auth B], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Focus chain D [auth B] Interactions & Density Focus chain C [auth B] Focus chain D [auth B]

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: 1.80 Å
R-Value Free: 0.246
R-Value Work: 0.219
R-Value Observed: 0.219
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.424	α = 90
b = 75.308	β = 90
c = 163.317	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Seetharaman, J.

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Database references, Structure summary
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

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.