4NI8 | pdb_00004ni8

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis complexed with Mn and 5-methoxyisophtalic acid

PDB DOI: https://doi.org/10.2210/pdb4NI8/pdb

Classification: LYASE
Organism(s): Sphingomonas paucimobilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-05 Released: 2014-11-26
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: 1.64 Å
R-Value Free:
0.175 (Depositor), 0.170 (DCC)
R-Value Work:
0.148 (Depositor), 0.150 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 5-carboxyvanillate decarboxylase LigW from Sphingomonas paucimobilis complexed with Mn and 5-methoxyisophtalic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 299.88 kDa
Atom Count: 23,932
Modeled Residue Count: 2,680
Deposited Residue Count: 2,680
Unique protein chains: 1

Macromolecules

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(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	Sphingomonas paucimobilis	Mutation(s): 0 Gene Names: ligW
UniProt
Find proteins for Q8RJ47 (Sphingomonas paucimobilis) Explore Q8RJ47 Go to UniProtKB: Q8RJ47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RJ47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1WB Query on 1WB Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain J [auth A] SDF format, chain KA [auth G] SDF format, chain P [auth B] SDF format, chain PA [auth H] SDF format, chain S [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] J [auth A] KA [auth G] P [auth B] AA [auth E], DA [auth F], J [auth A], KA [auth G], P [auth B], PA [auth H], S [auth C], X [auth D]	5-methoxybenzene-1,3-dicarboxylic acid C₉ H₈ O₅ POSMIIJADZKUPL-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain J [auth A] Focus chain KA [auth G] Focus chain P [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain J [auth A] Focus chain KA [auth G] Focus chain P [auth B] Focus chain PA [auth H] Focus chain S [auth C] Focus chain X [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain EA [auth F] MOL2 format, chain BA [auth E] MOL2 format, chain EA [auth F] mmCIF format, chain BA [auth E] mmCIF format, chain EA [auth F]	BA [auth E], EA [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain EA [auth F] Interactions & Density Focus chain BA [auth E] Focus chain EA [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain Q [auth B] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D]	FA [auth F] GA [auth F] HA [auth F] IA [auth F] K [auth A] FA [auth F], GA [auth F], HA [auth F], IA [auth F], K [auth A], L [auth A], LA [auth G], M [auth A], MA [auth G], N [auth A], NA [auth G], Q [auth B], QA [auth H], RA [auth H], T [auth C], U [auth C], V [auth C], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain FA [auth F] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain Q [auth B] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain JA [auth G] SDF format, chain O [auth B] SDF format, chain OA [auth H] SDF format, chain R [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain O [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain R [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain O [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain R [auth C] mmCIF format, chain W [auth D] mmCIF format, chain Z [auth E]	CA [auth F] I [auth A] JA [auth G] O [auth B] OA [auth H] CA [auth F], I [auth A], JA [auth G], O [auth B], OA [auth H], R [auth C], W [auth D], Z [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain JA [auth G] Focus chain O [auth B] Focus chain OA [auth H] Focus chain R [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain JA [auth G] Focus chain O [auth B] Focus chain OA [auth H] Focus chain R [auth C] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.175 (Depositor), 0.170 (DCC)
R-Value Work: 0.148 (Depositor), 0.150 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.523	α = 67.04
b = 99.896	β = 88.44
c = 100.427	γ = 68.07

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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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-11-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-11-26
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description