7P4W | pdb_00007p4w

Crystal structure of alpha-amylase from Aspergillus oryzae in space group I222


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

The FUSION protein crystallization screen.

Gorrec, F.Bellini, D.

(2022) J Appl Crystallogr 55: 310-319

  • DOI: https://doi.org/10.1107/S1600576722001765
  • Primary Citation Related Structures: 
    7P4W, 7P4Z

  • PubMed Abstract: 

    The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.


  • Organizational Affiliation
    • Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 53.01 kDa 
  • Atom Count: 3,785 
  • Modeled Residue Count: 476 
  • Deposited Residue Count: 476 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha-amylase476Aspergillus oryzaeMutation(s): 0 
EC: 3.2.1.1
UniProt
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P0C1B3 
Go to UniProtKB:  P0C1B3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C1B3
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth E]2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.285 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.238 (DCC) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.725α = 90
b = 140.402β = 90
c = 154.218γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary