4QRN | pdb_00004qrn

HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID

PDB DOI: https://doi.org/10.2210/pdb4QRN/pdb
Entry: 4QRN supersedes: 4ING

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Novosphingobium aromaticivorans DSM 12444
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-07-01 Released: 2014-08-06
Deposition Author(s): Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Gerlt, J.A., Raushel, F.M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free:
0.155 (Depositor), 0.144 (DCC)
R-Value Work:
0.135 (Depositor), 0.127 (DCC)
R-Value Observed:
0.136 (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 Novosphingobium Aromaticivorans

Patskovsky, Y., Vladimirova, A., Toro, R., Bhosle, R., Raushel, F.M., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 171.79 kDa
Atom Count: 13,693
Modeled Residue Count: 1,398
Deposited Residue Count: 1,492
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	373	Novosphingobium aromaticivorans DSM 12444	Mutation(s): 0 Gene Names: Saro_0799
UniProt
Find proteins for Q2GA79 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore Q2GA79 Go to UniProtKB: Q2GA79
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2GA79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1DF Query on 1DF Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain X [auth D] SDF format, chain R [auth C] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain X [auth D] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain X [auth D] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B]	F [auth A], N [auth B], R [auth C], X [auth D]	4-hydroxy-3-methoxy-5-nitrobenzoic acid C₈ H₇ N O₆ AEDVAGWYAKIOIM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] O [auth B] S [auth C] T [auth C] G [auth A], H [auth A], O [auth B], S [auth C], T [auth C], Y [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain W [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain W [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B], Q [auth C], W [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain W [auth D] Interactions & Density Focus chain E [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain W [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain P [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth D]	AA [auth D] I [auth A] J [auth A] K [auth A] P [auth B] AA [auth D], I [auth A], J [auth A], K [auth A], P [auth B], U [auth C], V [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.07 Å
R-Value Free: 0.155 (Depositor), 0.144 (DCC)
R-Value Work: 0.135 (Depositor), 0.127 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.723	α = 90
b = 60.747	β = 103.33
c = 130.517	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

This entry supersedes: 4ING

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description