[English] 日本語
Yorodumi
- PDB-1g6x: ULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g6x
TitleULTRA HIGH RESOLUTION STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) MUTANT WITH ALTERED BINDING LOOP SEQUENCE
ComponentsPANCREATIC TRYPSIN INHIBITOR
KeywordsHYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR
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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / EXISTING MODEL / Resolution: 0.86 Å
AuthorsAddlagatta, A. / Czapinska, H. / Krzywda, S. / Otlewski, J. / Jaskolski, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Ultrahigh-resolution structure of a BPTI mutant.
Authors: Addlagatta, A. / Krzywda, S. / Czapinska, H. / Otlewski, J. / Jaskolski, M.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: High-Resolution Structure of Bovine Pancreatic Trypsin Inhibitor with Altered Binding Loop Sequenc
Authors: Czapinska, H. / Otlewski, J. / Krzywda, S. / Sheldrick, G.M. / Jaskolski, M.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structure of Bovine Pancreatic Trypsin Inhibitor at 125 K: Definition of Carboxyl-Terminal Residues Gly57 and Ala58
Authors: Parkin, S. / Rupp, B. / Hope, H.
#3: Journal: J.Mol.Biol. / Year: 1992
Title: Determination of a High Quality Nuclear Magnetic Resonance Solution Structure of the Bovine Pancreatic Trypsin Inhibitor and Comparison with Three Crystal Structures
Authors: Berndt, K. / Guentert, P. / Orbons, L.P. / Wuethrich, K.
#4: Journal: J.Mol.Biol. / Year: 1984
Title: Structure of Bovine Pancreatic Trypsin Inhibitor . Results of Joint Neutron and X-Ray Refinement of Crystal Form II
Authors: Wlodawer, A. / Walter, J. / Huber, R. / Sjolin, L.
#5: Journal: Acta Crystallogr.,Sect.B / Year: 1975
Title: Crystallographic Refinement of the Structure of Bovine Pancreatic Trypsin Inhibitor at 1.5 A Resolution
Authors: Deisenhofer, J. / Steigemann, W.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,37411
Polymers6,4811
Non-polymers89310
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules

A: PANCREATIC TRYPSIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,74822
Polymers12,9632
Non-polymers1,78520
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4390 Å2
ΔGint-182 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.891, 51.891, 43.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-64-

SO4

21A-65-

SO4

31A-121-

HOH

41A-133-

HOH

51A-164-

HOH

61A-203-

HOH

-
Components

#1: Protein PANCREATIC TRYPSIN INHIBITOR / BPTI / APROTININ / TRASYLOL / BASIC PROTEASE INHIBITOR


Mass: 6481.481 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00974
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL ...Details: 2% PEG 400, 2 M AMMONIUM SULFATE, 0.1 M NA HEPES. A PROTEIN SAMPLE, LYOPHILIZED AFTER HPLC PURIFICATION FROM TFA/ACETONITRILE MIXTURE, WAS DISSOLVED IN WATER TO A CONCENTRATION OF 9 MG/2 UL DROPS OF THE PROTEIN SOLUTION WERE MIXED WITH 2 UL OF RESERVOIR SOLUTION CONTAINING 2% PEG 400, 2 M AMMONIUM SULFATE AND 0.1 M NA HEPES, PH 7.5. THE HANGING DROPLETS WERE EQUILIBRATED AT 19 DEG C THROUGH THE GAS PHASE WITH THE RESERVOIR. PRISMATIC CRYSTALS MEASURING UP TO 0.4 MM GREW WITHIN 12 HOURS. FOR LOW-TEMPERATURE DATA COLLECTION (100 K), THE CRYSTAL WAS CRYOPROTECTED IN THE RESERVOIR SOLUTION SUPPLEMENTED BY 30 % ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7 / Details: Czapinska, H., (2000) J.Mol.Biol., 295, 1237.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
22 %PEG4001reservoir
32.0 Mammonium sulfate1reservoir
40.1 Msodium HEPES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 7, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 0.86→20 Å / Num. obs: 47018 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 17.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 54.1
Reflection shellResolution: 0.86→0.9 Å / Redundancy: 6 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.61 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 814213
Reflection shell
*PLUS
% possible obs: 88.6 %

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: EXISTING MODEL
Starting model: 1QLQ

1qlq


Resolution: 0.86→10 Å / Num. parameters: 6499 / Num. restraintsaints: 7361 / Cross valid method: FREE R
StereochEM target val spec case: ETHYLENE GLYCOL (EDO) AND SULFATE (SO4) GEOMETRY BASED ON DATA FROM CSD
Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO ...Details: ANISOTROPIC REFINEMENT WITHOUT STEREOCHEMICAL RESTRAINTS ON ORDERED MAIN CHAIN. THE COMPLETE C-TERMINUS IS VISIBLE. IT FORMS A SALT-BRIDGE WITH THE N-TERMINUS. ARG 39 IS DISORDERED IN TWO CONFORMATIONS. IN ADDITION, IT IS ADJACENT TO CYS 38 OF THE DISORDERED 14-38 DISULFIDE AND IS PART OF A DISORDERED ARGININE CAGE. ALA 58 IS THE C-TERMINAL RESIDUE. IT IMMEDIATELY FOLLOWS THE DISORDERED GLY 56 - GLY 57 DOUBLET. THE CYS14-CYS38 DISULFIDE BRIDGE IS OBSERVED IN TWO DISTINCT CHIRALITIES (60 % RIGHT-HANDED, 40 % LEFT-HANDED). THE MAIN CHAIN OF THREE RESIDUES AND THE SIDE CHAINS OF 10 RESIDUES ARE MODELED IN TWO CONFORMATIONS. EIGHT SULFATE ANIONS (TWO WITH TWO-FOLD SYMMETRY) ARE PRESENT IN THE ASYMMETRIC UNIT. ONE OF THEM SHARES A SITE WITH THREE WATER MOLECULES. TWO ETHYLENE GLYCOL MOLECULES MODELED PER ONE PROTEIN MOLECULE. REFINEMENT CONCLUDED USING ONE CYCLE OF BLOCKED FULL-MATRIX LEAST-SQUARES ALGORITHM.
RfactorNum. reflection% reflectionSelection details
Rfree0.14 1883 4 %RANDOM
all0.1072 46998 --
obs0.1068 -94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 426 / Occupancy sum non hydrogen: 603
Refinement stepCycle: LAST / Resolution: 0.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms452 0 44 170 666
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.023
X-RAY DIFFRACTIONs_angle_d0.043
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.06
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.083
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.094
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor Rfree: 0.14 / Rfactor Rwork: 0.107
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.113

+
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