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), 0.230 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 CA [auth E] SDF format, chain GA [auth F] SDF format, chain V [auth C] SDF format, chain Y [auth D] SDF format, chain Q [auth B] SDF format, chain PA [auth H] SDF format, chain M [auth A] SDF format, chain JA [auth G] MOL2 format, chain CA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth G] mmCIF format, chain CA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth H] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth G]	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 DA [auth F] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain LA [auth H] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain DA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain LA [auth H] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain DA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain LA [auth H] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	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 AA [auth E] SDF format, chain BA [auth E] SDF format, chain FA [auth F] SDF format, chain U [auth C] SDF format, chain X [auth D] 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 IA [auth G] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain FA [auth F] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] 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 IA [auth G] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain FA [auth F] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] 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 IA [auth G]	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 HA [auth G] 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 EA [auth F] MOL2 format, chain HA [auth G] 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 EA [auth F] mmCIF format, chain HA [auth G] 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 EA [auth F]	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), 0.230 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (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

View Full Validation Report

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