2FCL | pdb_00002fcl

Crystal structure of a putative nucleotidyltransferase (tm1012) from Thermotoga maritima at 1.35 A resolution

PDB DOI: https://doi.org/10.2210/pdb2FCL/pdb

Classification: TRANSFERASE
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-12-12 Released: 2006-03-14
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.170 (Depositor), 0.184 (DCC)
R-Value Work:
0.140 (Depositor), 0.154 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of hypothetical protein (tm1012) from Thermotoga maritima at 1.35 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 20.62 kDa
Atom Count: 1,647
Modeled Residue Count: 157
Deposited Residue Count: 169
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein TM1012	A	169	Thermotoga maritima	Mutation(s): 0 Gene Names: tm1012
UniProt
Find proteins for Q9X0A5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0A5 Go to UniProtKB: Q9X0A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9X0A5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
UNL Query on UNL Download:Ideal Coordinates CCD File	B [auth A]	Unknown ligand LYCAIKOWRPUZTN-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
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.170 (Depositor), 0.184 (DCC)
R-Value Work: 0.140 (Depositor), 0.154 (DCC)
R-Value Observed: 0.142 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.769	α = 73.69
b = 36.382	β = 85.51
c = 39.785	γ = 78.97

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-03-14

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2006-03-14
Type: Initial release
Version 1.1: 2008-04-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-01-25
Changes: Database references, Derived calculations
Version 1.4: 2023-09-20
Changes: Data collection, Refinement description

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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.