7CT6 | pdb_00007ct6

Crystal structure of GCL from Deinococcus metallilatus

PDB DOI: https://doi.org/10.2210/pdb7CT6/pdb

Classification: LIGASE
Organism(s): Deinococcus metallilatus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-08-18 Released: 2021-08-25
Deposition Author(s): Kim, J.H., Kim, J.S.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.215 (Depositor), 0.220 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Glyoxylate carboligase-based whole-cell biotransformation of formaldehyde into ethylene glycol via glycolaldehyde.

Jo, H.J., Kim, J.H., Kim, Y.N., Seo, P.W., Kim, C.Y., Kim, J.W., Yu, H.N., Cheon, H.J., Lee, E.Y., Kim, J.S., Park, J.B.

(2022) Green Chem 1

DOI: https://doi.org/10.1039/D1GC03549E

Macromolecule Content

Total Structure Weight: 123.95 kDa
Atom Count: 8,916
Modelled Residue Count: 1,116
Deposited Residue Count: 1,116
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxylate carboligase	A, B	558	Deinococcus metallilatus	Mutation(s): 0 Gene Names: gcl, FCS05_00325 EC: 4.1.1.47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.215 (Depositor), 0.220 (DCC)
R-Value Work: 0.176 (Depositor), 0.190 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 148.055	α = 90
b = 106.469	β = 124.09
c = 89.093	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2021-08-25
Type: Initial release
Version 1.1: 2022-03-09
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary

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.