2ETD | pdb_00002etd

Crystal structure of a lema protein (tm0961) from thermotoga maritima msb8 at 2.28 A resolution

PDB DOI: https://doi.org/10.2210/pdb2ETD/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-10-27 Released: 2005-11-15
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free:
0.270 (Depositor), 0.284 (DCC)
R-Value Work:
0.216 (Depositor), 0.222 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 2ETD

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

Literature

Crystal structure of LEMA protein (tm0961) from THERMOTOGA MARITIMA at 2.28 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 19.98 kDa
Atom Count: 1,169
Modeled Residue Count: 141
Deposited Residue Count: 171
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lemA protein	A	171	Thermotoga maritima MSB8	Mutation(s): 16 Gene Names: tm0961
UniProt
Find proteins for Q9X056 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X056 Go to UniProtKB: Q9X056
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X056
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.28 Å
R-Value Free: 0.270 (Depositor), 0.284 (DCC)
R-Value Work: 0.216 (Depositor), 0.222 (DCC)

Diffraction Data:

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.454	α = 90
b = 85.259	β = 90
c = 53.397	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
HKL-2000	data scaling
SHELX	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-11-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2005-11-15
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-25
Changes: Author supporting evidence
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations

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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.