3KWX | pdb_00003kwx

Chemically modified Taka alpha-amylase

PDB DOI: https://doi.org/10.2210/pdb3KWX/pdb

Classification: HYDROLASE
Organism(s): Aspergillus oryzae
Mutation(s): No

Deposited: 2009-12-01 Released: 2009-12-29
Deposition Author(s): Siddiqui, K.S., Harrop, S.J., Poljak, A., De Francisci, D., Guerriero, G., Pilak, O., Burg, D., Raftery, M.J., Parkin, D.M., Trewhella, J., Cavicchioli, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.210 (Depositor), 0.206 (DCC)
R-Value Work:
0.175 (Depositor), 0.173 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

A Modified alpha-amylase with a molten-globule state has enhanced thermal stability

Siddiqui, K.S., Poljak, A., De Francisci, D., Guerriero, G., Pilak, O., Burg, D., Raftery, M.J., Parkin, D.M., Trewhella, J., Cavicchioli, R.

To be published.

Macromolecule Content

Total Structure Weight: 52.79 kDa
Atom Count: 3,977
Modeled Residue Count: 476
Deposited Residue Count: 478
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-amylase A type-1/2	A	478	Aspergillus oryzae	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C1B3
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.210 (Depositor), 0.206 (DCC)
R-Value Work: 0.175 (Depositor), 0.173 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.727	α = 90
b = 120.727	β = 90
c = 115.676	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-11-20
Changes: Structure summary