4L6D | pdb_00004l6d

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with vanillic acid

PDB DOI: https://doi.org/10.2210/pdb4L6D/pdb

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

Deposited: 2013-06-12 Released: 2013-11-13
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: 1.45 Å
R-Value Free:
0.168 (Depositor), 0.167 (DCC)
R-Value Work:
0.146 (Depositor), 0.144 (DCC)
R-Value Observed:
0.147 (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 from Sphingomonas paucimobilis complexed with vanillic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 302.51 kDa
Atom Count: 24,897
Modeled Residue Count: 2,680
Deposited Residue Count: 2,680
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RJ47
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain UA [auth H] SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain QA [auth G] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain GA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain UA [auth H] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain GA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain UA [auth H] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain GA [auth E]	BA [auth D] GA [auth E] LA [auth F] M [auth A] QA [auth G] BA [auth D], GA [auth E], LA [auth F], M [auth A], QA [auth G], S [auth B], UA [auth H], W [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain QA [auth G] Focus chain S [auth B] Focus chain UA [auth H] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain LA [auth F] Focus chain M [auth A] Focus chain QA [auth G] Focus chain S [auth B] Focus chain UA [auth H] Focus chain W [auth C]
VNL Query on VNL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain KA [auth F] SDF format, chain L [auth A] SDF format, chain NA [auth G] SDF format, chain P [auth B] SDF format, chain V [auth C] SDF format, chain Z [auth D] SDF format, chain U [auth C] SDF format, chain TA [auth H] SDF format, chain SA [auth H] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain PA [auth G] SDF format, chain OA [auth G] SDF format, chain K [auth A] SDF format, chain JA [auth F] SDF format, chain J [auth A] SDF format, chain FA [auth E] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain SA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain OA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain EA [auth E] mmCIF format, chain KA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain SA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain OA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] DA [auth E] EA [auth E] FA [auth E] J [auth A] AA [auth D], DA [auth E], EA [auth E], FA [auth E], J [auth A], JA [auth F], K [auth A], KA [auth F], L [auth A], NA [auth G], OA [auth G], P [auth B], PA [auth G], Q [auth B], R [auth B], SA [auth H], TA [auth H], U [auth C], V [auth C], Z [auth D]	4-HYDROXY-3-METHOXYBENZOATE C₈ H₇ O₄ WKOLLVMJNQIZCI-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth H] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain J [auth A] Focus chain JA [auth F] Focus chain K [auth A] Focus chain KA [auth F] Focus chain L [auth A] Focus chain NA [auth G] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain R [auth B] Focus chain SA [auth H] Focus chain TA [auth H] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain HA [auth E] MOL2 format, chain HA [auth E] mmCIF format, chain HA [auth E]	HA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain HA [auth E] Interactions & Density Focus chain HA [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth C] MOL2 format, chain X [auth C] mmCIF format, chain X [auth C]	X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain X [auth C] Interactions & Density Focus chain X [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain RA [auth H] SDF format, chain MA [auth G] SDF format, chain CA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain MA [auth G] MOL2 format, chain CA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain MA [auth G] mmCIF format, chain CA [auth E]	CA [auth E] I [auth A] IA [auth F] MA [auth G] N [auth A] CA [auth E], I [auth A], IA [auth F], MA [auth G], N [auth A], O [auth B], RA [auth H], T [auth C], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth B] Focus chain RA [auth H] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain MA [auth G] Focus chain N [auth A] Focus chain O [auth B] Focus chain RA [auth H] Focus chain T [auth C] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.168 (Depositor), 0.167 (DCC)
R-Value Work: 0.146 (Depositor), 0.144 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.592	α = 109.71
b = 96.917	β = 90.53
c = 97.029	γ = 111.89

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

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Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-11-13
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description