4QRO | pdb_00004qro

CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288) FROM POLAROMONAS SP. JS666 WITH BOUND MANGANESE AND AN INHIBITOR, 2-NITRORESORCINOL

PDB DOI: https://doi.org/10.2210/pdb4QRO/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Polaromonas sp. JS666
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, M., Almo, S.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.223 (Depositor), 0.234 (DCC)
R-Value Work:
0.189 (Depositor), 0.203 (DCC)
R-Value Observed:
0.190 (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 Dihydroxybenzoate Decarboxylase from Frompolaromonas Sp WITH BOUND MANGANESE AND 2-NITRORESORCINOL

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

To be published.

Macromolecule Content

Total Structure Weight: 324.62 kDa
Atom Count: 23,784
Modeled Residue Count: 2,603
Deposited Residue Count: 2,784
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-resorcylate decarboxylase	A, B, C, D, E A, B, C, D, E, F, G, H	348	Polaromonas sp. JS666	Mutation(s): 0 Gene Names: Bpro_2061 EC: 4.1.1.103
UniProt
Find proteins for Q12BV1 (Polaromonas sp. (strain JS666 / ATCC BAA-500)) Explore Q12BV1 Go to UniProtKB: Q12BV1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q12BV1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
38L Query on 38L Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain Y [auth D] SDF format, chain V [auth C] SDF format, chain PA [auth H] SDF format, chain M [auth A] SDF format, chain JA [auth G] SDF format, chain GA [auth F] SDF format, chain CA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain V [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain V [auth C] mmCIF format, chain PA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] GA [auth F] JA [auth G] M [auth A] PA [auth H] CA [auth E], GA [auth F], JA [auth G], M [auth A], PA [auth H], Q [auth B], V [auth C], Y [auth D]	2-nitrobenzene-1,3-diol C₆ H₅ N O₄ ZLCPKMIJYMHZMJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain M [auth A] Focus chain PA [auth H] Focus chain Q [auth B] Focus chain V [auth C] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain LA [auth H] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain DA [auth F] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth F] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth F]	DA [auth F] I [auth A] J [auth A] LA [auth H] N [auth B] DA [auth F], I [auth A], J [auth A], LA [auth H], N [auth B], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain DA [auth F] Focus chain I [auth A] Focus chain J [auth A] Focus chain LA [auth H] Focus chain N [auth B] Focus chain R [auth C]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain KA [auth G] MOL2 format, chain KA [auth G] mmCIF format, chain KA [auth G]	KA [auth G]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain KA [auth G] Interactions & Density Focus chain KA [auth G]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain IA [auth G] SDF format, chain X [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain P [auth B] SDF format, chain OA [auth H] SDF format, chain NA [auth H] SDF format, chain L [auth A] SDF format, chain FA [auth F] SDF format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain IA [auth G] MOL2 format, chain X [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain FA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain IA [auth G] mmCIF format, chain X [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain FA [auth F] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] FA [auth F] IA [auth G] L [auth A] AA [auth E], BA [auth E], FA [auth F], IA [auth G], L [auth A], NA [auth H], OA [auth H], P [auth B], T [auth C], U [auth C], X [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain L [auth A] Focus chain NA [auth H] Focus chain OA [auth H] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain X [auth D]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain O [auth B] SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain MA [auth H] SDF format, chain K [auth A] SDF format, chain HA [auth G] MOL2 format, chain EA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain MA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain HA [auth G] mmCIF format, chain EA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain MA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain HA [auth G]	EA [auth F] HA [auth G] K [auth A] MA [auth H] O [auth B] EA [auth F], HA [auth G], K [auth A], MA [auth H], O [auth B], S [auth C], W [auth D], Z [auth E]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain EA [auth F] Focus chain HA [auth G] Focus chain K [auth A] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain EA [auth F] Focus chain HA [auth G] Focus chain K [auth A] Focus chain MA [auth H] Focus chain O [auth B] Focus chain S [auth C] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.223 (Depositor), 0.234 (DCC)
R-Value Work: 0.189 (Depositor), 0.203 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.958	α = 90
b = 151.058	β = 92.15
c = 143.826	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	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):

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