6COC | pdb_00006coc

AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,F179L,A209I with benzaldehyde

PDB DOI: https://doi.org/10.2210/pdb6COC/pdb

Classification: LYASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-03-12 Released: 2019-03-20
Deposition Author(s): Jones, B.J., Kazlauskas, R.J., Desrouleaux, R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.190 (Depositor), 0.198 (DCC)
R-Value Work:
0.138 (Depositor), 0.151 (DCC)
R-Value Observed:
0.141 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

AtHNL enantioselectivity mutants

Jones, B.J., Desrouleaux, R., Kazlauskas, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 59.87 kDa
Atom Count: 4,651
Modeled Residue Count: 519
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-hydroxynitrile lyase	A, B	260	Arabidopsis thaliana	Mutation(s): 7 Gene Names: HNL, MES5, At5g10300, F18D22_70 EC: 4.1.2.10
UniProt
Find proteins for Q9LFT6 (Arabidopsis thaliana) Explore Q9LFT6 Go to UniProtKB: Q9LFT6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LFT6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HBX (Subject of Investigation/LOI) Query on HBX Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth B]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B]	benzaldehyde C₇ H₆ O HUMNYLRZRPPJDN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	C [auth A], D [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.190 (Depositor), 0.198 (DCC)
R-Value Work: 0.138 (Depositor), 0.151 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.56	α = 90
b = 86.72	β = 90
c = 122.03	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

Jones, B.J.

Kazlauskas, R.J.

Desrouleaux, R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM102205

Revision History (Full details and data files)

Version 1.0: 2019-03-20
Type: Initial release
Version 1.1: 2019-04-10
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description

6COC | pdb_00006coc

AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,F179L,A209I with benzaldehyde

Literature

AtHNL enantioselectivity mutants

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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