6PMU | pdb_00006pmu

Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae

PDB DOI: https://doi.org/10.2210/pdb6PMU/pdb

Classification: TRANSFERASE
Organism(s): Tetranychus urticae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-07-02 Released: 2020-07-08
Deposition Author(s): Daneshian, L., Schlachter, C., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.223 (Depositor)
R-Value Work:
0.180 (Depositor)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Structural Characterization of Beta Cyanoalanine Synthase from Tetranychus Urticae

Daneshian, L., Schlachter, C., Dermauw, W., Wybouw, N., Van Leeuwen, T., Chruszcz, M.

To be published.

Macromolecule Content

Total Structure Weight: 69.27 kDa
Atom Count: 4,514
Modeled Residue Count: 563
Deposited Residue Count: 642
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-cyanoalanine synthase	A, B	321	Tetranychus urticae	Mutation(s): 0 Gene Names: 107363798
UniProt
Find proteins for T1KF23 (Tetranychus urticae) Explore T1KF23 Go to UniProtKB: T1KF23
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T1KF23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.223 (Depositor)
R-Value Work: 0.180 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.387	α = 90
b = 91.387	β = 90
c = 137.426	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2020-07-08

Deposition Author(s):

Van Leeuwen, T.

Revision History (Full details and data files)

Version 1.0: 2020-07-08
Type: Initial release
Version 1.1: 2023-10-11
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.