9IZ5 | pdb_00009iz5

Multifunctional PLP-dependent enzyme TM1270

PDB DOI: https://doi.org/10.2210/pdb9IZ5/pdb

Classification: LYASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-07-31 Released: 2025-01-15
Deposition Author(s): Nitta, S., Miyamoto, T., Fushinobu, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.176 (Depositor), 0.185 (DCC)
R-Value Work:
0.150 (Depositor), 0.163 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Functional and Structural Analyses of a Highly Multifunctional Enzyme TM1270 from the Hyperthermophile Thermotoga maritima

Miyamoto, T., Nitta, S., Homma, H., Fushinobu, S.

(2024) ACS Catal 14: 18817-18830

DOI: https://doi.org/10.1021/acscatal.4c05275

Macromolecule Content

Total Structure Weight: 89.3 kDa
Atom Count: 6,518
Modeled Residue Count: 765
Deposited Residue Count: 784
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-alanine/L-glutamate racemase	A, B	392	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: aar, metC, TM_1270, Tmari_1275 EC: 5.1.1.1 (PDB Primary Data), 5.1.1.3 (PDB Primary Data)
UniProt
Find proteins for Q9X0Z7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0Z7 Go to UniProtKB: Q9X0Z7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9X0Z7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.176 (Depositor), 0.185 (DCC)
R-Value Work: 0.150 (Depositor), 0.163 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.418	α = 90
b = 120.578	β = 90
c = 137.067	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release

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.