[English] 日本語
Yorodumi
- PDB-3aub: A simplified BPTI variant stabilized by the A14G and A38V substit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3aub
TitleA simplified BPTI variant stabilized by the A14G and A38V substitutions
ComponentsBovine Pancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / Serine protease inhibitor / Trypsin
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular
Function and homology information
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsIslam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y.
CitationJournal: To be Published
Title: Effect of amino acid mutations of protein's solubility, function and structure characterized using short poly amino acid peptide tags
Authors: Islam, M.M. / Kato, A. / Khan, M.M.A. / Noguchi, K. / Yohda, M. / Kidokoro, S.I. / Kuroda, Y.
History
DepositionFeb 3, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bovine Pancreatic trypsin inhibitor
B: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)11,9742
Polymers11,9742
Non-polymers00
Water4,558253
1
A: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)5,9871
Polymers5,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bovine Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)5,9871
Polymers5,9871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.333, 39.058, 49.231
Angle α, β, γ (deg.)90.00, 101.59, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-161-

HOH

21B-235-

HOH

-
Components

#1: Protein Bovine Pancreatic trypsin inhibitor / BPTI


Mass: 5986.823 Da / Num. of mol.: 2 / Mutation: A14G, A38V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): JM109(DE3)PLYSS / Cellular location (production host): Inclusion body / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS SEQUENCE IS A SIMPLIFIED BPTI VARIANT WITH 21 ALANINES, AND IT HAS BEEN STABILIZED WITH THE ...THIS SEQUENCE IS A SIMPLIFIED BPTI VARIANT WITH 21 ALANINES, AND IT HAS BEEN STABILIZED WITH THE A14G AND A38V MUTATIONS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 15% PEG4000 ,15% Iisopropanol, 0.1M Sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 22, 2006
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→48.224 Å / Num. all: 53613 / Num. obs: 53613 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.294 / Rsym value: 0.243
Reflection shellResolution: 1→1.04 Å / Redundancy: 4 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 0.243 / Num. unique all: 53613 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
Cootmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PTI

4pti


Resolution: 1→48.22 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.672 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17931 2624 5.1 %RANDOM
Rwork0.16591 ---
obs0.16659 49180 96.63 %-
all-53613 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.401 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20.2 Å2
2--0.02 Å20 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms842 0 0 253 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022937
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.941286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.28820.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00815117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1421511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02787
X-RAY DIFFRACTIONr_nbd_refined0.1890.2485
X-RAY DIFFRACTIONr_nbtor_refined0.3160.2647
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.247
X-RAY DIFFRACTIONr_mcbond_it0.5951.5613
X-RAY DIFFRACTIONr_mcangle_it0.9042938
X-RAY DIFFRACTIONr_scbond_it1.3983376
X-RAY DIFFRACTIONr_scangle_it1.6384.5340
X-RAY DIFFRACTIONr_rigid_bond_restr1.0093989
X-RAY DIFFRACTIONr_sphericity_free1.773253
X-RAY DIFFRACTIONr_sphericity_bonded1.9443902
LS refinement shellResolution: 1→1.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1793 4433 -
Rwork0.1659 3046 -
obs-53613 96.6 %

+
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