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- PDB-2ker: alpha-amylase inhibitor Parvulustat (Z-2685) from Streptomyces pa... -

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Basic information

Entry
Database: PDB / ID: 2ker
Titlealpha-amylase inhibitor Parvulustat (Z-2685) from Streptomyces parvulus
ComponentsAlpha-amylase inhibitor Z-2685
KeywordsHYDROLASE INHIBITOR / alpha-amylase inhibitor / Parvulustat (Z-2685)
Function / homology
Function and homology information


alpha-amylase inhibitor activity
Similarity search - Function
Alpha-amylase inhibitor / Alpha-amylase inhibitor / Alpha-amylase inhibitor superfamily / Alpha amylase inhibitor / Alpha amylase inhibitor / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Alpha-amylase inhibitor Z-2685
Similarity search - Component
Biological speciesStreptomyces parvulus (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsRehm, S. / Han, S. / Hassani, I. / Sokocevic, A. / Jonker, H.R.A. / Engels, J.W. / Schwalbe, H.
CitationJournal: Chembiochem / Year: 2009
Title: The high resolution NMR structure of parvulustat (Z-2685) from Streptomyces parvulus FH-1641: comparison with tendamistat from Streptomyces tendae 4158
Authors: Rehm, S. / Han, S. / Hassani, I. / Sokocevic, A. / Jonker, H.R.A. / Engels, J.W. / Schwalbe, H.
History
DepositionFeb 2, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-amylase inhibitor Z-2685


Theoretical massNumber of molelcules
Total (without water)8,2911
Polymers8,2911
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Alpha-amylase inhibitor Z-2685 / Parvulustat


Mass: 8290.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces parvulus (bacteria) / Strain: FH-1641 / Production host: Streptomyces lividans (bacteria) / Strain (production host): TK24 / References: UniProt: P07512

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: High Resolution NMR solution structure of Parvulustat (Z-2685) from Streptomyces parvulus FH-1641
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1232D 1H-13C HSQC
1322D 1H-1H NOESY
1442D 1H-1H NOESY
1523D 1H-15N NOESY
1633D 1H-13C NOESY
1713D HNCO
1813D HN(CA)CB
1913D HBHA(CO)NH
11013D CBCA(CO)NH
11123D HNHA
11233D (H)CCH-TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] Parvulustat-1, 30 mM sodium phosphate-2, 170 mM sodium chloride-3, 0.01 % sodium azide-4, 92.5% H2O/7.5% D2O92.5% H2O/7.5% D2O
20.5 mM [U-100% 15N] Parvulustat-5, 30 mM sodium phosphate-6, 170 mM sodium chloride-7, 0.01 % sodium azide-8, 92.5% H2O/7.5% D2O92.5% H2O/7.5% D2O
30.5 mM [U-100% 13C; U-100% 15N] Parvulustat-9, 30 mM sodium phosphate-10, 170 mM sodium chloride-11, 0.01 % sodium azide-12, 100% D2O100% D2O
40.5 mM [U-100% 15N] Parvulustat-13, 30 mM sodium phosphate-14, 170 mM sodium chloride-15, 0.01 % sodium azide-16, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMParvulustat-1[U-100% 13C; U-100% 15N]1
30 mMsodium phosphate-21
170 mMsodium chloride-31
0.01 %sodium azide-41
0.5 mMParvulustat-5[U-100% 15N]2
30 mMsodium phosphate-62
170 mMsodium chloride-72
0.01 %sodium azide-82
0.5 mMParvulustat-9[U-100% 13C; U-100% 15N]3
30 mMsodium phosphate-103
170 mMsodium chloride-113
0.01 %sodium azide-123
0.5 mMParvulustat-13[U-100% 15N]4
30 mMsodium phosphate-144
170 mMsodium chloride-154
0.01 %sodium azide-164
Sample conditionsIonic strength: 200 / pH: 6.6 / Pressure: ambient / Temperature: 318 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
Sparky3.113Goddarddata analysis
Sparky3.113Goddardpeak picking
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1732 / NOE intraresidue total count: 526 / NOE long range total count: 713 / NOE medium range total count: 132 / NOE sequential total count: 361 / Hydrogen bond constraints total count: 38 / Protein phi angle constraints total count: 32 / Protein psi angle constraints total count: 32
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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