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- PDB-2laa: Solution Strucuture of the CBM25-1 of beta/alpha-amylase from Pae... -

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Basic information

Entry
Database: PDB / ID: 2laa
TitleSolution Strucuture of the CBM25-1 of beta/alpha-amylase from Paenibacillus polymyxa
ComponentsBeta/alpha-amylase
KeywordsHYDROLASE / SBD / CBM25
Function / homology
Function and homology information


beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / starch binding / alpha-amylase / alpha-amylase activity / polysaccharide catabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding module family 25 / Carbohydrate binding domain (family 25) / Carbohydrate binding domain / Glycoside hydrolase, family 14A, bacterial / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Alpha-amylase, C-terminal domain ...Carbohydrate binding module family 25 / Carbohydrate binding domain (family 25) / Carbohydrate binding domain / Glycoside hydrolase, family 14A, bacterial / Glycoside hydrolase, family 14, conserved site / Beta-amylase active site 1. / Beta-amylase active site 2. / Glycoside hydrolase, family 14 / Glycosyl hydrolase family 14 / Alpha-amylase, C-terminal domain / Aamy_C / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPaenibacillus polymyxa (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsHoribe, I. / Nishimura, S. / Takahashi, R. / Ohkubo, T. / Yoshida, T.
CitationJournal: To be Published
Title: A functional and structural analysis of tundem family 25 carbohydrate-binding modules from Paenibacillus polymyxa beta/alpha-amylase
Authors: Takahashi, R. / Horibe, I. / Fukada, H. / Yoshida, T. / Ohkubo, T. / Inui, T. / Nishimura, S. / Sumitani, J.
History
DepositionMar 9, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta/alpha-amylase


Theoretical massNumber of molelcules
Total (without water)10,7461
Polymers10,7461
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 2000target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Beta/alpha-amylase / Beta-amylase / Alpha-amylase


Mass: 10745.508 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 455-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus polymyxa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P21543, beta-amylase, alpha-amylase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D 1H-15N NOESY
1513D (H)CCH-TOCSY
1613D 1H-13C NOESY
1713D HNCO
1812D 1H-13C HSQC aromatic
1912D 1H-13C HSQC aliphatic
11013D 1H-15N TOCSY
11122D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-1.2 mM [U-100% 15N] sodium acetate-1, 0.5-1.2 mM [U-99% 13C; U-99% 15N] sodium acetate-2, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 15N] sodium acetate-3, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMsodium acetate-1[U-100% 15N]0.5-1.21
mMsodium acetate-2[U-99% 13C; U-99% 15N]0.5-1.21
0.6 mMsodium acetate-3[U-100% 15N]2
Sample conditionsIonic strength: 20 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
SPARKYGuntert, Braun and Wuthrichchemical shift assignment
DYANAGuntert, Braun and Wuthrichchemical shift assignment
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxcollection
DYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1728 / NOE intraresidue total count: 334 / NOE medium range total count: 900 / NOE sequential total count: 494
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 2000 / Conformers submitted total number: 20 / Representative conformer: 1

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