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- PDB-4bfh: Crystal structure of alpha-amylase inhibitor wrightide R1 (wR1) p... -

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Basic information

Entry
Database: PDB / ID: 4bfh
TitleCrystal structure of alpha-amylase inhibitor wrightide R1 (wR1) peptide from Wrightia religiosa
ComponentsWRIGHTIDE R1
KeywordsHYDROLASE INHIBITOR / INSECT ALPHA-AMYLASE INHIBITOR
Function / homologyAlpha amylase inhibitor Wrightide R1
Function and homology information
Biological speciesWRIGHTIA RELIGIOSA (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsYap, L.J. / Nguyen, P.Q.T. / Tam, J.P. / Lescar, J.
Citation
Journal: FEBS J. / Year: 2014
Title: Discovery and Characterization of Pseudocyclic Cystine-Knot Alpha-Amylase Inhibitors with High Resistance to Heat and Proteolytic Degradation.
Authors: Nguyen, P.Q. / Wang, S. / Kumar, A. / Yap, L.J. / Luu, T.T. / Lescar, J. / Tam, J.P.
#1: Journal: Structure / Year: 1999
Title: Specific Inhibition of Insect Alpha-Amylases: Yellow Meal Worm Alpha-Amylase in Complex with the Amaranth Alpha-Amylase Inhibitor at 2.0 A Resolution.
Authors: Pereira, P.J. / Lozanov, V. / Patthy, A. / Huber, R. / Bode, W. / Pongor, S. / Strobl, S.
History
DepositionMar 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Oct 15, 2014Group: Database references
Revision 1.4Mar 18, 2015Group: Database references
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WRIGHTIDE R1


Theoretical massNumber of molelcules
Total (without water)3,2561
Polymers3,2561
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)16.194, 29.133, 47.701
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/peptide WRIGHTIDE R1


Mass: 3255.765 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ALPHA-AMYLASE INHIBITOR / Source: (natural) WRIGHTIA RELIGIOSA (plant) / References: UniProt: V5W9K8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.73 Å3/Da / Density % sol: 28.82 % / Description: NONE
Crystal growpH: 2 / Details: pH 2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→25 Å / Num. obs: 6362 / % possible obs: 95.4 % / Observed criterion σ(I): 66 / Redundancy: 3.3 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.2
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 11.9 / % possible all: 90.3

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLV

1clv


Resolution: 1.25→24.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.2 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.15927 317 5 %RANDOM
Rwork0.15779 ---
obs0.15787 6017 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.25→24.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms223 0 0 41 264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022231
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.967316
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.735529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.76825.5569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.261533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.233
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021178
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2731.5149
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.5882239
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.94382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4844.577
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.4493231
X-RAY DIFFRACTIONr_sphericity_free0.75341
X-RAY DIFFRACTIONr_sphericity_bonded0.6863223
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 22 -
Rwork0.164 412 -
obs--100 %

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