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- PDB-1b1u: CRYSTAL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR RAGI -

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Basic information

Entry
Database: PDB / ID: 1b1u
TitleCRYSTAL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR RAGI
ComponentsPROTEIN (ALPHA-AMYLASE/TRYPSIN INHIBITOR RATI)
KeywordsHYDROLASE INHIBITOR / ALPHA-AMYLASE/TRYPSIN INHIBITOR (RATI) / BIFUNCTIONAL
Function / homology
Function and homology information


alpha-amylase inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal trypsin/alpha-amylase inhibitors family signature. / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-amylase/trypsin inhibitor
Similarity search - Component
Biological speciesEleusine coracana (finger millet)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGourinath, S. / Srinivasan, A. / Singh, T.P.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of the bifunctional inhibitor of trypsin and alpha-amylase from ragi seeds at 2.2 A resolution.
Authors: Gourinath, S. / Alam, N. / Srinivasan, A. / Betzel, C. / Singh, T.P.
#1: Journal: Biochemistry / Year: 1995
Title: Determination of the Three-Dimensional Structure of the Bifunctional Alpha-Amylase/Trypsin Inhibitor from Ragi Seeds by NMR Spectroscopy
Authors: Strobl, S. / Muhlhahn, P. / Bernstein, R. / Wiltscheck, R. / Maskos, K. / Wunderlich, M. / Huber, R. / Glockshuber, R. / Holak, T.A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Preliminary X-Ray Investigation of a Bifunctional Inhibitor from Indian Finger Millet (Ragi)
Authors: Srinivasan, A. / Raman, A. / Singh, T.P.
#3: Journal: FEBS Lett. / Year: 1983
Title: The Complete Amino Acid Sequence of the Bifunctional Alpha-Amylase/Trypsin Inhibitor from Seeds of Ragi (Indian Finger Millet, Eleusine Coracana Gaertn.)
Authors: Campos, F.A.P. / Richardson, M.
History
DepositionNov 23, 1998Processing site: RCSB
SupersessionDec 2, 1998ID: 1JFO
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 13, 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: PROTEIN (ALPHA-AMYLASE/TRYPSIN INHIBITOR RATI)


Theoretical massNumber of molelcules
Total (without water)13,1531
Polymers13,1531
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.380, 54.480, 40.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTEIN (ALPHA-AMYLASE/TRYPSIN INHIBITOR RATI) / RAGI BIFUNCTIONAL INHIBITOR


Mass: 13153.313 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Eleusine coracana (finger millet) / Organ: SEED / References: UniProt: P01087
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growpH: 8
Details: 1.15M AMMONIUM SULFATE, 0.2M AMMONIUM PHOSPHATE PH 8.0
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mMsodium phosphate11pH8.0
20.3 Mammonium sulfate11
310-15 mg/mlprotein11
41.15 Mammonium sulfate12
50.4 Msodium phosphate12pH8.0

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 5684 / % possible obs: 98.7 % / Redundancy: 12.2 % / Biso Wilson estimate: 25.4 Å2 / Rsym value: 0.094 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.27 / Rsym value: 0.299 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / Num. obs: 5094 / % possible obs: 91 % / Num. measured all: 57852 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.79 Å / % possible obs: 83.5 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 2.27

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoRE(CCP4)phasing
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BIP, MODEL 20

1bip


Resolution: 2.2→10 Å / Rfactor Rfree error: 0.023 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.321 251 5.6 %RANDOM
Rwork0.222 ---
obs0.222 4451 79.7 %-
Displacement parametersBiso mean: 24.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms880 0 0 88 968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.77
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.91.5
X-RAY DIFFRACTIONx_mcangle_it4.572
X-RAY DIFFRACTIONx_scbond_it3.992
X-RAY DIFFRACTIONx_scangle_it5.162.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 26 5 %
Rwork0.295 498 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARA-1.DATTOPO-1.DAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 5094 / Rfactor all: 0.224 / Rfactor obs: 0.219 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.2
LS refinement shell
*PLUS
Highest resolution: 2.2 Å

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