6B2F | pdb_00006b2f

Phosphotriesterase variant S5 + TS analogue

PDB DOI: https://doi.org/10.2210/pdb6B2F/pdb

Classification: HYDROLASE
Organism(s): Brevundimonas diminuta
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-09-20 Released: 2019-01-23
Deposition Author(s): Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (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

Phosphotriesterase variant S5 + TS analogue

Miton, C.M., Campbell, E.C., Jackson, C.J., Tokuriki, N.

To be published.

Macromolecule Content

Total Structure Weight: 73.25 kDa
Atom Count: 5,427
Modeled Residue Count: 644
Deposited Residue Count: 666
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotriesterase	A, B [auth G]	333	Brevundimonas diminuta	Mutation(s): 0 EC: 3.1.8.1
UniProt
Find proteins for A0A060GYS1 (Brevundimonas diminuta) Explore A0A060GYS1 Go to UniProtKB: A0A060GYS1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A060GYS1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HLN (Subject of Investigation/LOI) Query on HLN Download:Ideal Coordinates CCD File SDF format, chain M [auth G] SDF format, chain F [auth A] MOL2 format, chain M [auth G] MOL2 format, chain F [auth A] mmCIF format, chain M [auth G] mmCIF format, chain F [auth A]	F [auth A], M [auth G]	hexyl(naphthalen-2-yloxy)phosphinic acid C₁₆ H₂₁ O₃ P UBECMGZHZQOIIW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth G] Interactions & Density Focus chain F [auth A] Focus chain M [auth G]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain N [auth G] SDF format, chain L [auth G] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth G] MOL2 format, chain L [auth G] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth G] mmCIF format, chain L [auth G] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A] G [auth A] H [auth A] I [auth A] L [auth G] E [auth A], G [auth A], H [auth A], I [auth A], L [auth G], N [auth G]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth G] Focus chain N [auth G] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth G] Focus chain N [auth G]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth G] SDF format, chain J [auth G] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth G] MOL2 format, chain J [auth G] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth G] mmCIF format, chain J [auth G] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth G], K [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth G] Focus chain K [auth G] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth G] Focus chain K [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B [auth G]	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.230 (Depositor), 0.229 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.66	α = 90
b = 85.02	β = 90
c = 87.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-01-23
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection