[English] 日本語
Yorodumi
- PDB-1bhc: BOVINE PANCREATIC TRYPSIN INHIBITOR CRYSTALLIZED FROM THIOCYANATE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bhc
TitleBOVINE PANCREATIC TRYPSIN INHIBITOR CRYSTALLIZED FROM THIOCYANATE
ComponentsBOVINE PANCREATIC TRYPSIN INHIBITOR
KeywordsPROTEASE INHIBITOR / TRYPSIN
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
THIOCYANATE ION / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHamiaux, C. / Prange, T.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: The decameric structure of bovine pancreatic trypsin inhibitor (BPTI) crystallized from thiocyanate at 2.7 A resolution.
Authors: Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A. / Lafont, S. / Astier, J.P. / Veesler, S.
#1: Journal: J.Cryst.Growth / Year: 1997
Title: Comparison of Solubilities and Molecular Interactions of Bpti Molecules Giving Different Polymorphs
Authors: Lafont, S. / Veesler, S. / Astier, J.P. / Boistelle, R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Structure of Hexagonal Turkey Egg-White Lysozyme at 1.65 A Resolution
Authors: Howell, P.L.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of a Dimeric Form of Erabutoxin-B, Crystallized from a Thiocyanate Solution
Authors: Saludjian, P. / Prange, T. / Navaza, J. / Menez, R. / Guilloteau, J.P. / Ries-Kautt, M. / Ducruix, A.
#4: Journal: J.Mol.Biol. / Year: 1987
Title: Comparison of Two Highly Refined Structures of Bovine Pancreatic Trypsin Inhibitor
Authors: Wlodawer, A. / Deisenhofer, J. / Huber, R.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Sep 16, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BOVINE PANCREATIC TRYPSIN INHIBITOR
B: BOVINE PANCREATIC TRYPSIN INHIBITOR
C: BOVINE PANCREATIC TRYPSIN INHIBITOR
D: BOVINE PANCREATIC TRYPSIN INHIBITOR
E: BOVINE PANCREATIC TRYPSIN INHIBITOR
F: BOVINE PANCREATIC TRYPSIN INHIBITOR
G: BOVINE PANCREATIC TRYPSIN INHIBITOR
H: BOVINE PANCREATIC TRYPSIN INHIBITOR
I: BOVINE PANCREATIC TRYPSIN INHIBITOR
J: BOVINE PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,85720
Polymers65,27610
Non-polymers58110
Water2,126118
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18410 Å2
ΔGint-93 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.560, 73.830, 64.470
Angle α, β, γ (deg.)90.00, 93.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.322539, -0.743759, -0.585483), (0.789341, 0.552717, -0.267292), (0.522408, -0.375934, 0.765352)14.7897, -14.6813, -9.5362
2given(-0.796878, -0.429776, -0.424593), (0.537888, -0.184727, -0.822528), (0.275069, -0.883838, 0.378376)36.6469, -8.1341, -3.6496
3given(-0.81782, 0.517475, 0.251773), (-0.404327, -0.205365, -0.89126), (-0.409499, -0.830689, 0.377181)34.8033, 10.713, 10.0257
4given(0.303358, 0.79397, 0.526863), (-0.743767, 0.542925, -0.389928), (-0.595638, -0.273576, 0.755229)12.0803, 15.6931, 12.3294
5given(0.233894, 0.745194, 0.624484), (0.747183, -0.548744, 0.374964), (0.622102, 0.378902, -0.685144)15.9196, 13.1271, -47.4288
6given(-0.847758, 0.430328, 0.310039), (0.418914, 0.184749, 0.889033), (0.325296, 0.883564, -0.336893)37.8741, 18.3952, -42.5223
7given(-0.76984, -0.522255, -0.366872), (-0.528382, 0.199095, 0.825332), (-0.357992, 0.829223, -0.429222)38.239, 36.9402, -28.9267
8given(0.384392, -0.793618, -0.471607), (-0.785383, -0.549622, 0.284762), (-0.485198, 0.260932, -0.834564)16.3103, 43.9961, -25.0799
9given(0.990971, 0.001274, 0.134068), (0.000921, -0.999996, 0.002692), (0.134071, -0.002544, -0.990968)2.4046, 28.9818, -36.9897

-
Components

#1: Protein
BOVINE PANCREATIC TRYPSIN INHIBITOR / BPTI


Mass: 6527.568 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: PANCREAS / References: UniProt: P00974
#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.61 Å3/Da / Density % sol: 52 %
Crystal growpH: 4.5
Details: BPTI WAS CRYSTALLIZED FROM 250MM THIOCYANATE IN ACETATE BUFFER (50MM, PH=4.5)
Crystal grow
*PLUS
Method: other / Details: Lafont, S., (1997) J. Crystal Growth, 173, 132.

-
Data collection

DiffractionMean temperature: 292 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.63→29.59 Å / Num. obs: 18308 / % possible obs: 85.5 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 11.1
Reflection shellResolution: 2.63→2.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.186 / % possible all: 13.4
Reflection
*PLUS
Num. measured all: 69959
Reflection shell
*PLUS
% possible obs: 13.4 %

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA-AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6PTI

6pti


Resolution: 2.7→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUES ARG1, ASP3, LYS15, LYS26 AND ARG39 APPEAR TO HAVE NCS BREAKDOWN IN RELATED MOLECULES. THEY WERE REMOVED FROM THE NCS RESTRAINT SCHEME. MET 52 WAS MODELLED WITH TWO CONFORMATIONS IN ...Details: RESIDUES ARG1, ASP3, LYS15, LYS26 AND ARG39 APPEAR TO HAVE NCS BREAKDOWN IN RELATED MOLECULES. THEY WERE REMOVED FROM THE NCS RESTRAINT SCHEME. MET 52 WAS MODELLED WITH TWO CONFORMATIONS IN ALL MOLECULES. 10 THIOCYANATE IONS AND 118 WATER MOLECULES ARE GIVEN FOLLOWING THE COORDINATES OF THE TEN MOLECULES. AS IN 6PTI, NO DENSITY WAS OBSERVED FOR THE TWO LAST RESIDUES (GLY 57 & ALA 58).
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1753 9.6 %RANDOM
Rwork0.201 ---
obs0.201 17808 97.9 %-
Displacement parametersBiso mean: 25.65 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.27 Å
Luzzati d res low-10 Å
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4490 0 30 118 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.45
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.31.5
X-RAY DIFFRACTIONx_mcangle_it4.92
X-RAY DIFFRACTIONx_scbond_it5.62
X-RAY DIFFRACTIONx_scangle_it8.62.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)Weight Biso Weight position
11RESTRAINTS6.890.0672150
228.260.112375
336.860.28310
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 222 9.85 %
Rwork0.295 1957 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.SCNTOPH19.SCN
Software
*PLUS
Name: X-PLOR / Version: 3.01 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.45
LS refinement shell
*PLUS
Rfactor Rfree: 0.4

+
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