3X3H | pdb_00003x3h

Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) 3KP (K176P, K199P, K224P) triple mutant

PDB DOI: https://doi.org/10.2210/pdb3X3H/pdb
Entry: 3X3H supersedes: 3RKT

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

Deposited: 2015-01-21 Released: 2016-03-02
Deposition Author(s): Cielo, C.B.C., Yamane, T., Asano, Y., Dadashipour, M., Suzuki, A., Mizushima, T., Komeda, H., Okazaki, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.204 (Depositor), 0.210 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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., Okazaki, S.

To be published.

Macromolecule Content

Total Structure Weight: 234.5 kDa
Atom Count: 16,544
Modeled Residue Count: 2,064
Deposited Residue Count: 2,064
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-hydroxynitrile lyase	A, B, C, D, E A, B, C, D, E, F, G, H	258	Manihot esculenta	Mutation(s): 3 Gene Names: HNL EC: 4.1.2.47
UniProt
Find proteins for P52705 (Manihot esculenta) Explore P52705 Go to UniProtKB: P52705
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P52705
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.88 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.204 (Depositor), 0.210 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.04	α = 90
b = 84.21	β = 90.2
c = 134.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
MOLREP	phasing
REFMAC	refinement
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Dadashipour, M.

This entry supersedes: 3RKT

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

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.