6E6I | pdb_00006e6i

Crystal structure of 4-methyl HOPDA bound to LigY from Sphingobium sp. strain SYK-6

PDB DOI: https://doi.org/10.2210/pdb6E6I/pdb

Classification: HYDROLASE
Organism(s): Sphingobium sp. SYK-6
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-07-24 Released: 2019-01-30
Deposition Author(s): Kuatsjah, E., Chan, A.C., Hurst, T.E., Snieckus, V., Murphy, M.E., Eltis, L.D.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.219 (Depositor), 0.228 (DCC)
R-Value Work:
0.183 (Depositor), 0.194 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Metal- and Serine-Dependent Meta-Cleavage Product Hydrolases Utilize Similar Nucleophile-Activation Strategies

Kuatsjah, E., Chan, A.C.K., Hurst, T.E., Snieckus, V., Murphy, M.E.P., Eltis, L.D.

(2018) ACS Catal 8: 11622-11632

DOI: https://doi.org/10.1021/acscatal.8b02955

Macromolecule Content

Total Structure Weight: 338.59 kDa
Atom Count: 24,473
Modeled Residue Count: 2,985
Deposited Residue Count: 2,988
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl meta-cleavage compound hydrolase	A, B, C, D, E A, B, C, D, E, F, G, H, I	332	Sphingobium sp. SYK-6	Mutation(s): 0 Gene Names: ligY, SLG_07750
UniProt
Find proteins for A0ACD6B9C3 (Sphingobium sp. (strain NBRC 103272 / SYK-6)) Explore A0ACD6B9C3 Go to UniProtKB: A0ACD6B9C3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9C3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HVS (Subject of Investigation/LOI) Query on HVS Download:Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain W [auth G] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth I]	AA [auth I] K [auth A] M [auth B] O [auth C] Q [auth D] AA [auth I], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	(1Z,3E)-5-carboxy-3-methyl-5-oxo-1-phenylpenta-1,3-dien-1-olate C₁₃ H₁₁ O₄ JCSKQBIZFFCCKU-UVTPKQPNSA-M		Interactions Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain Z [auth I] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain Z [auth I] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.219 (Depositor), 0.228 (DCC)
R-Value Work: 0.183 (Depositor), 0.194 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.645	α = 90
b = 195.099	β = 90
c = 179.917	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	04802
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	171359

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description