[English] 日本語
Yorodumi
- PDB-1b0c: EVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b0c
TitleEVIDENCE OF A COMMON DECAMER IN THREE CRYSTAL STRUCTURES OF BPTI, CRYSTALLIZED FROM THIOCYANATE, CHLORIDE OR SULFATE
ComponentsPROTEIN (PANCREATIC TRYPSIN INHIBITOR)
KeywordsHYDROLASE INHIBITOR / BOVINE PANCREATIC TRYPSIN INHIBITOR / PENTAMERIC MOLECULE
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...: / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The BPTI decamer observed in acidic pH crystal forms pre-exists as a stable species in solution.
Authors: Hamiaux, C. / Perez, J. / Prange, T. / Veesler, S. / Ries-Kautt, M. / Vachette, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The Decameric Structure of Bovine Pancreatic Trypsin Inhibitor (Bpti) Crystallized from Thiocyanate at 2.7A Resolution
Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Decamers Observed in the Crystals of Bovine Panreatic Trypsin Inhibitor
Authors: Lubkowski, J. / Wlodawer, A.
History
DepositionNov 6, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)32,6385
Polymers32,6385
Non-polymers00
Water1,04558
1
A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)

A: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
B: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
C: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
D: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)
E: PROTEIN (PANCREATIC TRYPSIN INHIBITOR)


Theoretical massNumber of molelcules
Total (without water)65,27610
Polymers65,27610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)95.470, 95.470, 159.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.936918, -0.279679, -0.209678), (0.292717, 0.299889, 0.907956), (-0.191056, -0.912056, 0.362838)26.8161, -46.825, 84.2046
2given(0.844053, -0.179696, -0.505257), (0.167754, -0.806422, 0.567047), (-0.509346, -0.563377, -0.650518)46.8711, 20.9744, 152.3607
3given(0.839134, 0.175766, -0.514743), (-0.171677, -0.812391, -0.557269), (-0.516121, 0.555992, -0.65153)34.6748, 110.901, 111.4845
4given(0.939976, 0.277804, -0.198169), (-0.282692, 0.308661, -0.908193), (-0.191132, 0.9097, 0.368667)5.5089, 97.8479, 16.9573

-
Components

#1: Protein
PROTEIN (PANCREATIC TRYPSIN INHIBITOR) / BASIC PROTEASE INHIBITOR / BPI / BPTI / APROTININ


Mass: 6527.568 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.23 Å3/Da / Density % sol: 61 %
Crystal growpH: 4.5
Details: ACETATE BUFFER PH=4.5 BPTI 60 TO 100 MG/ML NACL 1.6 TO 2 M
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMsodium acetate1reservoir
260-100 mg/mlinhibitor1drop
31.6-2 M1dropNaCl

-
Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 1997 / Details: MIRRORS
RadiationMonochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→18 Å / Num. obs: 11127 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.038 / Net I/σ(I): 17.2
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 5.4 / Rsym value: 0.14 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.77 Å / % possible obs: 89.3 % / Num. measured all: 107368 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 2.77 Å / Lowest resolution: 2.84 Å / % possible obs: 55.5 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.7

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
Agrovatadata reduction
ROTAVATAdata reduction
AMoREphasing
X-PLOR3.851refinement
Agrovatadata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PTI

6pti


Resolution: 2.8→18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1125 10.3 %RANDOM
Rwork0.198 ---
obs0.198 10908 98 %-
Displacement parametersBiso mean: 37.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 0 58 2186
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_d23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.13
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight position
11CONSTRX-RAY DIFFRACTION0.0294300
22X-RAY DIFFRACTION0.0266300
33X-RAY DIFFRACTION0.0286300
44X-RAY DIFFRACTION0.0258300
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.348 108 10.2 %
Rwork0.3 950 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.3

+
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