3RKS | pdb_00003rks

Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) K176P mutant

PDB DOI: https://doi.org/10.2210/pdb3RKS/pdb

Classification: LYASE
Organism(s): Manihot esculenta
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-04-18 Released: 2012-06-20
Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.174 (Depositor), 0.177 (DCC)
R-Value Observed:
0.177 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3RKS

This is version 1.1 of the entry. See complete history.

Literature

Crystallographic Studies of Manihot esculenta hydroxynitrile lyase Lysine-to-Proline mutants

Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H.

To be published.

Macromolecule Content

Total Structure Weight: 117.69 kDa
Atom Count: 8,807
Modeled Residue Count: 1,032
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydroxynitrilase	A, B, C, D	258	Manihot esculenta	Mutation(s): 1 Gene Names: HNL EC: 4.1.2.37 (PDB Primary Data), 4.1.2.47 (UniProt)
UniProt
Find proteins for P52705 (Manihot esculenta) Explore P52705 Go to UniProtKB: P52705
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52705
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth D] MOL2 format, chain E [auth C] MOL2 format, chain F [auth D] mmCIF format, chain E [auth C] mmCIF format, chain F [auth D]	E [auth C], F [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth D] Interactions & Density Focus chain E [auth C] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.174 (Depositor), 0.177 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.628	α = 90
b = 91.414	β = 90
c = 137.441	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-20

Deposition Author(s):

Dadashipour, M.

Revision History (Full details and data files)

Version 1.0: 2012-06-20
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.