[English] 日本語
Yorodumi
- PDB-1b1u: CRYSTAL STRUCTURE OF THE BIFUNCTIONAL INHIBITOR RAGI -

+
Open data


ID or keywords:

Loading...

-
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 seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Cereal trypsin/alpha-amylase inhibitors family signature. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more