[English] 日本語
Yorodumi
- PDB-1a0l: HUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a0l
TitleHUMAN BETA-TRYPTASE: A RING-LIKE TETRAMER WITH ACTIVE SITES FACING A CENTRAL PORE
ComponentsBETA-TRYPTASE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / TRYPSIN-LIKE SERINE PROTEINASE / TETRAMER / HEPARIN / ALLERGY / ASTHMA / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


tryptase / serine-type peptidase activity / collagen-containing extracellular matrix / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-APA / Tryptase beta-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPereira, P.J.B. / Bergner, A. / Macedo-Ribeiro, S. / Huber, R. / Matschiner, G. / Fritz, H. / Sommerhoff, C.P. / Bode, W.
CitationJournal: Nature / Year: 1998
Title: Human beta-tryptase is a ring-like tetramer with active sites facing a central pore.
Authors: Pereira, P.J. / Bergner, A. / Macedo-Ribeiro, S. / Huber, R. / Matschiner, G. / Fritz, H. / Sommerhoff, C.P. / Bode, W.
History
DepositionDec 3, 1997Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-TRYPTASE
B: BETA-TRYPTASE
C: BETA-TRYPTASE
D: BETA-TRYPTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4108
Polymers109,5774
Non-polymers8334
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-33 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.930, 82.930, 172.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.960332, 0.276891, -0.033061), (0.275832, 0.925793, -0.258505), (-0.04097, -0.25737, -0.965444)132.62109, 5.2743, 181.90961
2given(-0.999796, -0.001683, 0.020114), (0.007034, -0.9631, 0.269053), (0.018919, 0.269139, 0.962915)140.32651, 43.3124, -7.408
3given(0.961787, -0.270732, 0.040859), (-0.270396, -0.962653, -0.013641), (0.043026, 0.002071, -0.999072)8.4737, 87.6665, 170.3678

-
Components

#1: Protein
BETA-TRYPTASE


Mass: 27394.311 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: IN COMPLEX WITH AMIDINO PHENYL PYRUVIC ACID (APPA), A SYNTHETIC INHIBITOR
Source: (natural) Homo sapiens (human) / Cell: MAST CELL / Organ: LUNG / References: UniProt: P20231, tryptase
#2: Chemical
ChemComp-APA / (2S)-3-(4-carbamimidoylphenyl)-2-hydroxypropanoic acid


Mass: 208.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsFOR ALL FOUR CHAINS, THE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA IS COVALENTLY CONNECTED TO THE ...FOR ALL FOUR CHAINS, THE C2 ATOM OF P-AMIDINO-PHENYL-PYRUVATE APA IS COVALENTLY CONNECTED TO THE CORRESPONDING SER195 SIDE CHAIN ATOM OG, FORMING HEMIKETAL.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50 %
Crystal growpH: 5 / Details: pH 5.0
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Msodium chloride1drop
23 Mammonium sulfate1reservoir
30.2 M3-(N-morpholino)propanesulphonic acid1reservoir

-
Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.121
Reflection
*PLUS
Num. obs: 23164

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→10 Å / Data cutoff high absF: 10000000000 / Data cutoff low absF: 0 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 -5 %RANDOM
Rwork0.197 ---
obs0.197 22536 99.3 %-
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 60 96 7872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg2.004
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.69
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.434
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 NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.449 -5.7 %
Rwork0.316 2089 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19X.PRO
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_deg24.69
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.434
LS refinement shell
*PLUS
Rfactor obs: 0.316

+
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