4ICM | pdb_00004icm

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis

PDB DOI: https://doi.org/10.2210/pdb4ICM/pdb

Classification: LYASE
Organism(s): Sphingobium sp. SYK-6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-12-10 Released: 2013-12-11
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Vladimirova, A., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.205 (Depositor), 0.210 (DCC)
R-Value Work:
0.163 (Depositor), 0.160 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis

Fedorov, A.A., Fedorov, E.V., Vladimirova, A., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 297.3 kDa
Atom Count: 23,188
Modeled Residue Count: 2,680
Deposited Residue Count: 2,680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-carboxyvanillate decarboxylase	A, B, C, D, E A, B, C, D, E, F, G, H	335	Sphingobium sp. SYK-6	Mutation(s): 0 Gene Names: ligW, SLG_07850
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth C] MOL2 format, chain L [auth C] mmCIF format, chain L [auth C]	L [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth C] Interactions & Density Focus chain L [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain S [auth H] SDF format, chain P [auth F] MOL2 format, chain S [auth H] MOL2 format, chain P [auth F] mmCIF format, chain S [auth H] mmCIF format, chain P [auth F]	P [auth F], S [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth F] Focus chain S [auth H] Interactions & Density Focus chain P [auth F] Focus chain S [auth H]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain R [auth H] SDF format, chain Q [auth G] SDF format, chain O [auth F] SDF format, chain N [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain O [auth F] MOL2 format, chain N [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain R [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain O [auth F] mmCIF format, chain N [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] M [auth D] N [auth E] I [auth A], J [auth B], K [auth C], M [auth D], N [auth E], O [auth F], Q [auth G], R [auth H]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain R [auth H]