1DWI

Study on radiation damage on a cryocooled crystal. Part 5: Structure after irradiation with 54.0*10e15 photons/mm2

• PDB DOI: https://doi.org/10.2210/pdb1DWI/pdb

• Classification: HYDROLASE
• Organism(s): Sinapis alba
• Mutation(s): No 


• Deposited: 1999-12-05 Released: 2000-03-03 
• Deposition Author(s): Burmeister, W.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.285 
• R-Value Work: 0.280 
• R-Value Observed: 0.280 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 62.37 kDa 
• Atom Count: 5,220 
• Modelled Residue Count: 499 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYROSINASE MA1	A [auth M]	499	Sinapis alba	Mutation(s): 0  EC: 3.2.1.147
UniProt
Find proteins for P29736 (Sinapis alba) Explore P29736  Go to UniProtKB:  P29736

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A], E [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G06206UV GlyCosmos:  G06206UV GlyGen:  G06206UV

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	7		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G26295XE GlyCosmos:  G26295XE GlyGen:  G26295XE

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth M], G [auth M], H [auth M], I [auth M], J [auth M], K [auth M]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	M, N [auth M], O [auth M], P [auth M], Q [auth M], R [auth M], S [auth M], T [auth M]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	U [auth M], V [auth M], W [auth M], X [auth M], Y [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	L [auth M]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.285 
• R-Value Work: 0.280 
• R-Value Observed: 0.280 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.3	α = 90
b = 136.4	β = 90
c = 80.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-03 
Deposition Author(s): Burmeister, W.P.

Revision History  

• Version 1.0: 2000-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-20
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.2: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary