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), 0.206 (DCC)
R-Value Work:
0.163 (Depositor), 0.163 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4ICM

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:

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
UniProt
Find proteins for A0ACD6B9C4 (Sphingobium sp. (strain NBRC 103272 / SYK-6)) Explore A0ACD6B9C4 Go to UniProtKB: A0ACD6B9C4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9C4
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 P [auth F] SDF format, chain S [auth H] MOL2 format, chain P [auth F] MOL2 format, chain S [auth H] mmCIF format, chain P [auth F] mmCIF format, chain S [auth H]	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 I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth H] SDF format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] MOL2 format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H] mmCIF format, chain J [auth B]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.205 (Depositor), 0.206 (DCC)
R-Value Work: 0.163 (Depositor), 0.163 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.817	α = 109.58
b = 96.897	β = 90.48
c = 97.004	γ = 111.66

Software Package:

Software Name	Purpose
CBASS	data collection
BALBES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-12-11

Deposition Author(s):

Vladimirova, A.

Revision History (Full details and data files)

Version 1.0: 2013-12-11
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.