3H3E

Crystal structure of Tm1679, A METAL-DEPENDENT HYDROLASE OF THE BETA-LACTAMASE SUPERFAMILY

PDB DOI: https://doi.org/10.2210/pdb3H3E/pdb

Classification: structural genomics, METAL BINDING PROTEIN
Organism(s): Thermotoga maritima
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-04-16 Released: 2009-07-14
Deposition Author(s): Cooper, D.R., Olekhnovitch, N., Derewenda, U., Derewenda, Z.S., Integrated Center for Structure and Function Innovation (ISFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.207
R-Value Work: 0.151
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of Tm1679, A METAL-DEPENDENT HYDROLASE OF THE BETA-LACTAMASE SUPERFAMILY

Cooper, D.R., Olekhnovitch, N., Derewenda, Z.S.

To be published.

Macromolecule Content

Total Structure Weight: 30.55 kDa
Atom Count: 2,123
Modelled Residue Count: 256
Deposited Residue Count: 267
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 protein Tm1679	A	267	Thermotoga maritima	Mutation(s): 2 Gene Names: TM_1679
UniProt
Find proteins for Q9X207 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X207 Go to UniProtKB: Q9X207
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X207
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.75 Å
R-Value Free: 0.207
R-Value Work: 0.151
R-Value Observed: 0.151
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.169	α = 90
b = 127.169	β = 90
c = 41.044	γ = 120

Software Package:

Software Name	Purpose
SOLVE	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Olekhnovitch, N.

Derewenda, Z.S.

Integrated Center for Structure and Function Innovation (ISFI)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations

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.