9DR5 | pdb_00009dr5

Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound, P1 form)

PDB DOI: https://doi.org/10.2210/pdb9DR5/pdb

Classification: HYDROLASE
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-09-25 Released: 2024-10-02
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.183 (Depositor), 0.189 (DCC)
R-Value Work:
0.151 (Depositor), 0.159 (DCC)
R-Value Observed:
0.152 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of Catechol 1,2-dioxygenase from Burkholderia multivorans (Zinc bound, P1 form)

Enayati, P., Liu, L., Lovell, S., Buchko, G.W., Battaile, K.P.

To be published.

Macromolecule Content

Total Structure Weight: 284.96 kDa
Atom Count: 22,348
Modeled Residue Count: 2,477
Deposited Residue Count: 2,552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol 1,2-dioxygenase	A, B, C, D, E A, B, C, D, E, F, G, H	319	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: catA EC: 1.13.11.1
UniProt
Find proteins for A0A0H3KXJ8 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KXJ8 Go to UniProtKB: A0A0H3KXJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3KXJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
12P Query on 12P Download:Ideal Coordinates CCD File SDF format, chain AB [auth H] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain OA [auth F] SDF format, chain UA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain OA [auth F] MOL2 format, chain UA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] mmCIF format, chain AB [auth H] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain OA [auth F] mmCIF format, chain UA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	AB [auth H] J [auth A] K [auth A] NA [auth F] OA [auth F] AB [auth H], J [auth A], K [auth A], NA [auth F], OA [auth F], UA [auth G], V [auth C], W [auth C]	DODECAETHYLENE GLYCOL C₂₄ H₅₀ O₁₃ WRZXKWFJEFFURH-UHFFFAOYSA-N		Interactions Focus chain AB [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain AB [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain NA [auth F] Focus chain OA [auth F] Focus chain UA [auth G] Focus chain V [auth C] Focus chain W [auth C]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain CA [auth D] SDF format, chain HA [auth E] SDF format, chain L [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain VA [auth G] SDF format, chain X [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth C] mmCIF format, chain BB [auth H] mmCIF format, chain CA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain VA [auth G] mmCIF format, chain X [auth C]	BB [auth H] CA [auth D] HA [auth E] L [auth A] PA [auth F] BB [auth H], CA [auth D], HA [auth E], L [auth A], PA [auth F], Q [auth B], VA [auth G], X [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain BB [auth H] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain VA [auth G] Focus chain X [auth C] Interactions & Density Focus chain BB [auth H] Focus chain CA [auth D] Focus chain HA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain VA [auth G] Focus chain X [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth D] SDF format, chain FB [auth H] SDF format, chain LA [auth E] SDF format, chain O [auth A] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain YA [auth G] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain FB [auth H] MOL2 format, chain LA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain YA [auth G] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain FB [auth H] mmCIF format, chain LA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain SA [auth F] mmCIF format, chain T [auth B] mmCIF format, chain YA [auth G]	AA [auth C] FA [auth D] FB [auth H] LA [auth E] O [auth A] AA [auth C], FA [auth D], FB [auth H], LA [auth E], O [auth A], SA [auth F], T [auth B], YA [auth G]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain LA [auth E] Focus chain O [auth A] Focus chain SA [auth F] Focus chain T [auth B] Focus chain YA [auth G] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth D] Focus chain FB [auth H] Focus chain LA [auth E] Focus chain O [auth A] Focus chain SA [auth F] Focus chain T [auth B] Focus chain YA [auth G]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain EB [auth H] SDF format, chain KA [auth E] MOL2 format, chain EB [auth H] MOL2 format, chain KA [auth E] mmCIF format, chain EB [auth H] mmCIF format, chain KA [auth E]	EB [auth H], KA [auth E]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain EB [auth H] Focus chain KA [auth E] Interactions & Density Focus chain EB [auth H] Focus chain KA [auth E]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain GA [auth E] SDF format, chain I [auth A] SDF format, chain MA [auth F] SDF format, chain P [auth B] SDF format, chain TA [auth G] SDF format, chain U [auth C] SDF format, chain ZA [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain TA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain ZA [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain TA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain ZA [auth H]	BA [auth D] GA [auth E] I [auth A] MA [auth F] P [auth B] BA [auth D], GA [auth E], I [auth A], MA [auth F], P [auth B], TA [auth G], U [auth C], ZA [auth H]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain P [auth B] Focus chain TA [auth G] Focus chain U [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain GA [auth E] Focus chain I [auth A] Focus chain MA [auth F] Focus chain P [auth B] Focus chain TA [auth G] Focus chain U [auth C] Focus chain ZA [auth H]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain DA [auth D] SDF format, chain DB [auth H] SDF format, chain EA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain QA [auth F] SDF format, chain R [auth B] SDF format, chain RA [auth F] SDF format, chain S [auth B] SDF format, chain WA [auth G] SDF format, chain XA [auth G] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain DB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain QA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth F] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] mmCIF format, chain CB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain DB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain QA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain RA [auth F] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	CB [auth H] DA [auth D] DB [auth H] EA [auth D] IA [auth E] CB [auth H], DA [auth D], DB [auth H], EA [auth D], IA [auth E], JA [auth E], M [auth A], N [auth A], QA [auth F], R [auth B], RA [auth F], S [auth B], WA [auth G], XA [auth G], Y [auth C], Z [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CB [auth H] Focus chain DA [auth D] Focus chain DB [auth H] Focus chain EA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain QA [auth F] Focus chain R [auth B] Focus chain RA [auth F] Focus chain S [auth B] Focus chain WA [auth G] Focus chain XA [auth G] Focus chain Y [auth C] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.183 (Depositor), 0.189 (DCC)
R-Value Work: 0.151 (Depositor), 0.159 (DCC)
R-Value Observed: 0.152 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.97	α = 106.04
b = 86.27	β = 96.74
c = 110.161	γ = 113.15

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394