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- PDB-1ok0: Crystal Structure of Tendamistat -

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Basic information

Entry
Database: PDB / ID: 1ok0
TitleCrystal Structure of Tendamistat
ComponentsALPHA-AMYLASE INHIBITOR HOE-467A
KeywordsINHIBITOR / ALPHA AMYLASE INHIBITOR
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 HOE-467A
Similarity search - Component
Biological speciesSTREPTOMYCES TENDAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.93 Å
AuthorsKoenig, V. / Vertesy, L. / Schneider, T.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystal Structure of the Alpha-Amylase Inhibitor Tendamistat at 0.93 A
Authors: Koenig, V. / Vertesy, L. / Schneider, T.R.
History
DepositionJul 16, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-AMYLASE INHIBITOR HOE-467A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1874
Polymers7,9681
Non-polymers2203
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)25.680, 40.780, 60.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-AMYLASE INHIBITOR HOE-467A / TENDAMISTAT


Mass: 7967.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES TENDAE (bacteria) / Strain: 4158 / References: UniProt: P01092
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAMMALIAN ALPHA-AMYLASES, BUT DOES NOT INHIBIT PLANT AND MICROBIAL ALPHA-AMYLASES. KNOWN TO FORM A ...MAMMALIAN ALPHA-AMYLASES, BUT DOES NOT INHIBIT PLANT AND MICROBIAL ALPHA-AMYLASES. KNOWN TO FORM A 1:1 COMPLEX WITH ALPHA-AMYLASE
Has protein modificationY
Sequence detailsTHE SEQUENCE CONFLICT IS DESCRIBED IN THE REFERENCES THAT ACCOMPANY THE SWS ENTRY P01092

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.58 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 1.5
Details: 20MG OF LYOPHILIZED PROTEIN WERE DISSOLVED IN 1ML OF DOUBLE-DISTILLED WATER. USING THE HANGING DROP METHOD WITH DROPS OF 2MUL PROTEIN SOLUTION (20 MG/ML) AND 2MUL RESERVOIR SOLUTION (0.1-0.5 ...Details: 20MG OF LYOPHILIZED PROTEIN WERE DISSOLVED IN 1ML OF DOUBLE-DISTILLED WATER. USING THE HANGING DROP METHOD WITH DROPS OF 2MUL PROTEIN SOLUTION (20 MG/ML) AND 2MUL RESERVOIR SOLUTION (0.1-0.5 M NACL ADJUSTED TO PH 1.3 WITH HYDROCHLORIC ACID), YIELDED TUFT-SHAPED AGGLOMERATES OF ESSENTIALLY ONE-DIMENSIONAL CRYSTALS. STREAK SEEDING {EM VIA} A CAT WHISKER AFTER TOUCHING THESE AGGLOMERATES GAVE SINGLE CRYSTALS WITH DIMENSIONS UP TO 0.1 X 0.01 X 0.01MM^3
Crystal grow
*PLUS
pH: 1.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
20.1-0.5 M1reservoirpH1.3NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.911
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.911 Å / Relative weight: 1
ReflectionResolution: 0.93→40 Å / Num. obs: 261064 / % possible obs: 93.5 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.3
Reflection shellResolution: 0.93→0.95 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.3 / % possible all: 79.9
Reflection
*PLUS
Highest resolution: 0.93 Å / Lowest resolution: 40 Å / Num. obs: 41072 / Redundancy: 6.9 % / Num. measured all: 261064 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 79.9 % / Redundancy: 3.5 % / Num. unique obs: 2167 / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HOE

1hoe


Resolution: 0.93→10 Å / Num. parameters: 7433 / Num. restraintsaints: 10184 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.13 5 5 %RANDOM
all0.1029 2054 --
obs0.1026 -93.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 15
Refinement stepCycle: LAST / Resolution: 0.93→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms558 0 13 159 730
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.341
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.033
X-RAY DIFFRACTIONs_approx_iso_adps0.087
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 41006 / Rfactor Rwork: 0.1026
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.341
X-RAY DIFFRACTIONs_chiral_restr0.082

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