[English] 日本語
Yorodumi
- PDB-1pbi: CRYSTAL STRUCTURE OF A BOWMAN-BIRK INHIBITOR FROM PEA SEEDS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pbi
TitleCRYSTAL STRUCTURE OF A BOWMAN-BIRK INHIBITOR FROM PEA SEEDS
ComponentsBOWMAN-BIRK PROTEINASE INHIBITOR
KeywordsBOWMAN-BIRK INHIBITOR / TRYPSIN INHIBITOR / CHYMOTRYPSIN INHIBITOR
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cysteine Protease (Bromelain) Inhibitor, subunit H / Cysteine Protease (Bromelain) Inhibitor, subunit H / Bowman-Birk serine protease inhibitor family / Proteinase inhibitor I12, Bowman-Birk / Bowman-Birk type proteinase inhibitor / Bowman-Birk type proteinase inhibitor / Ribbon / Mainly Beta
Similarity search - Domain/homology
Seed trypsin/chymotrypsin inhibitor IVB
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi De La Sierra, I. / Brunie, S.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Dimeric crystal structure of a Bowman-Birk protease inhibitor from pea seeds.
Authors: Li de la Sierra, I. / Quillien, L. / Flecker, P. / Gueguen, J. / Brunie, S.
History
DepositionAug 20, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BOWMAN-BIRK PROTEINASE INHIBITOR
B: BOWMAN-BIRK PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)15,8602
Polymers15,8602
Non-polymers00
Water59433
1
A: BOWMAN-BIRK PROTEINASE INHIBITOR
B: BOWMAN-BIRK PROTEINASE INHIBITOR

A: BOWMAN-BIRK PROTEINASE INHIBITOR
B: BOWMAN-BIRK PROTEINASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)31,7204
Polymers31,7204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)52.680, 52.680, 135.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.984559, 0.017231, -0.174206), (0.022898, -0.99927, 0.030574), (-0.173552, -0.03409, -0.984235)2.5513, 53.9906, 37.0665
2given(0.982488, 0.056156, -0.17766), (0.052951, -0.998338, -0.022733), (-0.178642, 0.012927, -0.983829)1.8079, 53.9992, 36.1165

-
Components

#1: Protein BOWMAN-BIRK PROTEINASE INHIBITOR


Mass: 7930.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Organ: SEEDS / References: UniProt: P56679
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.64 %(v/v)PEG4001drop
36x10-5 Mcalcium chloride1drop
40.032 MNa-HEPES1drop
52 %PEG4001reservoir
61.4 Mammonium sulfate1reservoir
70.1 MNa-HEPES1reservoir

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.39
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1996
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.39 Å / Relative weight: 1
ReflectionResolution: 2.62→13.9 Å / Num. obs: 5770 / % possible obs: 95.2 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 51.9 Å2 / Rsym value: 0.054
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.188 / % possible all: 59.7
Reflection
*PLUS
Num. measured all: 22543 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 59.7 % / Rmerge(I) obs: 0.188

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEITdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
SCALEITdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: X-RAY COORDINATES OF BOWMAN-BIRK INHIBITOR FROM SOYBEAN

Resolution: 2.7→7 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: RESOLUTION-DEPENDENT WEIGHTING
RfactorNum. reflection% reflectionSelection details
Rfree0.272 561 10.9 %RANDOM
Rwork0.214 ---
obs0.214 5141 96.5 %-
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 0 33 1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_d29.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.021.5
X-RAY DIFFRACTIONx_mcangle_it4.932
X-RAY DIFFRACTIONx_scbond_it42
X-RAY DIFFRACTIONx_scangle_it5.542.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.7→2.86 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 90 10.8 %
Rwork0.33 744 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor obs: 0.33

+
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://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