4YK7 | pdb_00004yk7

Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)

PDB DOI: https://doi.org/10.2210/pdb4YK7/pdb

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

Deposited: 2015-03-04 Released: 2016-04-13
Deposition Author(s): Dadashipour, M., Nakano, S., Asano, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.262 (Depositor), 0.244 (DCC)
R-Value Work:
0.240 (Depositor), 0.220 (DCC)
R-Value Observed:
0.241 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4YK7

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

Literature

Crystal structure of S-hydroxynitrile lyase from Manihot esculenta (His103Leu)

Dadashipour, M., Nakano, S., Asano, Y.

To be published.

Macromolecule Content

Total Structure Weight: 117.53 kDa
Atom Count: 8,348
Modeled Residue Count: 1,032
Deposited Residue Count: 1,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(S)-hydroxynitrile lyase	A, B, C, D	258	Manihot esculenta	Mutation(s): 1 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52705
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.262 (Depositor), 0.244 (DCC)
R-Value Work: 0.240 (Depositor), 0.220 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.469	α = 90
b = 88.098	β = 90
c = 135.213	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Dadashipour, M.

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Derived calculations
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Refinement description

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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.