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

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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

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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.