7DIB | pdb_00007dib

Crystal structure of D-threonine aldolase from Filomicrobium marinum

PDB DOI: https://doi.org/10.2210/pdb7DIB/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Candidatus Filomicrobium marinum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-11-18 Released: 2021-08-04
Deposition Author(s): Seo, H., Kim, K.-J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.254 (Depositor), 0.258 (DCC)
R-Value Work:
0.211 (Depositor), 0.218 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7DIB

This is version 1.1 of the entry. See complete history.

Literature

Cbeta-Selective Aldol Addition of d-Threonine Aldolase by Spatial Constraint of Aldehyde Binding.

Park, S.-H., Seo, H., Seok, J., Kim, H., Kwon, K.K., Yeom, S.-J., Lee, S.-G., Kim, K.-J.

(2021) ACS Catal 11: 6892-6899

DOI: https://doi.org/10.1021/acscatal.1c01348

Macromolecule Content

Total Structure Weight: 84.99 kDa
Atom Count: 5,632
Modeled Residue Count: 740
Deposited Residue Count: 792
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-threonine aldolase	A, B	396	Candidatus Filomicrobium marinum	Mutation(s): 0 Gene Names: YBN1229_v1_3680 EC: 4.1.2.42
UniProt
Find proteins for A0A0D6JKM4 (Candidatus Filomicrobium marinum) Explore A0A0D6JKM4 Go to UniProtKB: A0A0D6JKM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D6JKM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.20 Å
R-Value Free: 0.254 (Depositor), 0.258 (DCC)
R-Value Work: 0.211 (Depositor), 0.218 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.965	α = 90
b = 178.051	β = 90
c = 65.458	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.