4NG3 | pdb_00004ng3

Crystal structure of 5-carboxyvanillate decarboxylase from Sphingomonas paucimobilis complexed with 4-Hydroxy-3-methoxy-5-nitrobenzoic acid

PDB DOI: https://doi.org/10.2210/pdb4NG3/pdb
Entry: 4NG3 supersedes: 4L5P

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

Deposited: 2013-11-01 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: 1.75 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.152 (Depositor), 0.150 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
View more details

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 4-Hydroxy-3-methoxy-5-nitrobenzoic acid

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

To be published.

Macromolecule Content

Total Structure Weight: 299.74 kDa
Atom Count: 23,979
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
1DF Query on 1DF Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain M [auth B] SDF format, chain J [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain M [auth B] MOL2 format, chain J [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain V [auth E] mmCIF format, chain M [auth B] mmCIF format, chain J [auth A]	BA [auth F] EA [auth G] HA [auth H] J [auth A] M [auth B] BA [auth F], EA [auth G], HA [auth H], J [auth A], M [auth B], P [auth C], S [auth D], V [auth E]	4-hydroxy-3-methoxy-5-nitrobenzoic acid C₈ H₇ N O₆ AEDVAGWYAKIOIM-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain V [auth E]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain IA [auth H] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain N [auth B] SDF format, chain CA [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain N [auth B] MOL2 format, chain CA [auth F] mmCIF format, chain IA [auth H] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain N [auth B] mmCIF format, chain CA [auth F]	CA [auth F], IA [auth H], N [auth B], W [auth E], X [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain IA [auth H] Focus chain N [auth B] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain CA [auth F] Focus chain IA [auth H] Focus chain N [auth B] Focus chain W [auth E] Focus chain X [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain JA [auth H] SDF format, chain K [auth A] SDF format, chain KA [auth H] SDF format, chain T [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain Q [auth C] SDF format, chain FA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain Q [auth C] MOL2 format, chain FA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth H] mmCIF format, chain T [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain Q [auth C] mmCIF format, chain FA [auth G]	FA [auth G] JA [auth H] K [auth A] KA [auth H] Q [auth C] FA [auth G], JA [auth H], K [auth A], KA [auth H], Q [auth C], T [auth D], Y [auth E], Z [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain Q [auth C] Focus chain T [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain FA [auth G] Focus chain JA [auth H] Focus chain K [auth A] Focus chain KA [auth H] Focus chain Q [auth C] Focus chain T [auth D] Focus chain Y [auth E] Focus chain Z [auth E]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain GA [auth H] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain U [auth E] SDF format, chain L [auth B] SDF format, chain I [auth A] SDF format, chain DA [auth G] MOL2 format, chain AA [auth F] MOL2 format, chain GA [auth H] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain U [auth E] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth G] mmCIF format, chain AA [auth F] mmCIF format, chain GA [auth H] mmCIF format, chain O [auth C] mmCIF format, chain R [auth D] mmCIF format, chain U [auth E] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth G]	AA [auth F] DA [auth G] GA [auth H] I [auth A] L [auth B] AA [auth F], DA [auth G], GA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.152 (Depositor), 0.150 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.544	α = 66.64
b = 100.399	β = 67.96
c = 100.024	γ = 88.24

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-11-13

Deposition Author(s):

This entry supersedes: 4L5P

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