[English] 日本語
Yorodumi
- PDB-4m7g: Streptomyces Erythraeus Trypsin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4m7g
TitleStreptomyces Erythraeus Trypsin
ComponentsTrypsin-like protease
KeywordsHYDROLASE / Serine Protease
Function / homology
Function and homology information


trypsin / serine-type endopeptidase activity / proteolysis
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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...: / 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
Trypsin / Trypsin-like protease
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.81 Å
AuthorsBlankenship, E. / Vukoti, K. / Miyagi, M. / Lodowski, D.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Conformational flexibility in the catalytic triad revealed by the high-resolution crystal structure of Streptomyces erythraeus trypsin in an unliganded state.
Authors: Blankenship, E. / Vukoti, K. / Miyagi, M. / Lodowski, D.T.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trypsin-like protease


Theoretical massNumber of molelcules
Total (without water)23,3411
Polymers23,3411
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.958, 61.249, 74.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Trypsin-like protease


Mass: 23340.789 Da / Num. of mol.: 1 / Fragment: UNP residues 43-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Plasmid: PQE-80L / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q54137, UniProt: P24664*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / pH: 7.9
Details: 10 mM calcium chloride, 100 mM HEPES pH 7.0, 2.72 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.688
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2012
RadiationMonochromator: CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.688 Å / Relative weight: 1
ReflectionResolution: 0.79→61.38 Å / Num. obs: 234158 / % possible obs: 99.8 %
Reflection shellResolution: 0.79→0.83 Å / Redundancy: 5.1 % / % possible all: 96.9

-
Processing

Software
NameVersionClassification
XDSdata scaling
ARP/wARPmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SGT

1sgt


Resolution: 0.81→47.22 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.286 / SU ML: 0.008 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.009 / ESU R Free: 0.01 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.12 11678 5 %RANDOM
Rwork0.109 ---
obs0.112 220874 99.5 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0 Å2
2--0.45 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.81→47.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 0 0 353 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191959
X-RAY DIFFRACTIONr_bond_other_d0.0020.021829
X-RAY DIFFRACTIONr_angle_refined_deg2.0321.9542717
X-RAY DIFFRACTIONr_angle_other_deg3.09934221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.12726.83579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20215299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.924154
X-RAY DIFFRACTIONr_chiral_restr0.1240.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212438
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0110.9471060
X-RAY DIFFRACTIONr_mcbond_other0.9420.9381059
X-RAY DIFFRACTIONr_mcangle_it1.2651.431367
X-RAY DIFFRACTIONr_mcangle_other1.5131324
X-RAY DIFFRACTIONr_scbond_it2.1311.184899
X-RAY DIFFRACTIONr_scbond_other1.709877
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0661.6011317
X-RAY DIFFRACTIONr_long_range_B_refined2.9839.1862528
X-RAY DIFFRACTIONr_long_range_B_other2.4468.3752289
X-RAY DIFFRACTIONr_rigid_bond_restr5.71231959
X-RAY DIFFRACTIONr_sphericity_free20.091550
X-RAY DIFFRACTIONr_sphericity_bonded9.89752194
LS refinement shellResolution: 0.81→0.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 874 -
Rwork0.341 15727 -
obs--96.86 %

+
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://pdbjlc1.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