[English] 日本語
Yorodumi
- PDB-5fss: Structure of thermolysin prepared by the 'soak-and-freeze' method... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fss
TitleStructure of thermolysin prepared by the 'soak-and-freeze' method under 40 bar of krypton pressure
ComponentsTHERMOLYSIN
KeywordsHYDROLASE / METALLOPROTEINASE / THERMOLYSINE / KRYPTON / PRESSURE / FLASH FREEZING
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
KRYPTON / LYSINE / VALINE / Thermolysin
Similarity search - Component
Biological speciesBACILLUS THERMOPROTEOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
CitationJournal: J.Appl.Crystallogr. / Year: 2016
Title: Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionJan 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Structure summary
Revision 1.2May 10, 2017Group: Structure summary
Revision 1.3Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17512
Polymers34,3601
Non-polymers81511
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.749, 92.749, 128.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2012-

HOH

21A-2183-

HOH

31A-2186-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein THERMOLYSIN / THERMOSTABLE NEUTRAL PROTEINASE


Mass: 34360.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THERMOPROTEOLYTICUS (bacteria)
Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: P00800, thermolysin

-
Non-polymers , 7 types, 343 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Kr
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6
Details: 1:1 WITH 50MM MES PH6, 1MNACL 45%(V/V) DMSO RESERVOIR: 35% SATURATED AMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.861
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.5→46.37 Å / Num. obs: 52712 / % possible obs: 99.5 % / Observed criterion σ(I): 7.9 / Redundancy: 34.9 % / Biso Wilson estimate: 14.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.3
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 35.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 6.7 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DO1

3do1


Resolution: 1.5→46.375 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 2582 4.9 %
Rwork0.1615 --
obs0.1624 52712 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 31 332 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082568
X-RAY DIFFRACTIONf_angle_d1.1933505
X-RAY DIFFRACTIONf_dihedral_angle_d13.252892
X-RAY DIFFRACTIONf_chiral_restr0.046374
X-RAY DIFFRACTIONf_plane_restr0.007464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5290.2271500.19022682X-RAY DIFFRACTION98
1.529-1.56020.19671480.18142710X-RAY DIFFRACTION99
1.5602-1.59410.19461400.17932735X-RAY DIFFRACTION99
1.5941-1.63120.21931300.17162733X-RAY DIFFRACTION99
1.6312-1.6720.21191340.17382750X-RAY DIFFRACTION99
1.672-1.71720.17161500.16632727X-RAY DIFFRACTION99
1.7172-1.76770.21171210.16382747X-RAY DIFFRACTION99
1.7677-1.82480.18091430.1622764X-RAY DIFFRACTION100
1.8248-1.890.18891420.16392747X-RAY DIFFRACTION100
1.89-1.96570.18221590.1592746X-RAY DIFFRACTION100
1.9657-2.05510.20541370.15952775X-RAY DIFFRACTION100
2.0551-2.16350.17081490.14982766X-RAY DIFFRACTION100
2.1635-2.2990.16911430.15662796X-RAY DIFFRACTION100
2.299-2.47650.15671380.15972818X-RAY DIFFRACTION100
2.4765-2.72570.19281620.1592811X-RAY DIFFRACTION100
2.7257-3.12010.17731590.16662836X-RAY DIFFRACTION100
3.1201-3.93070.16971280.15472902X-RAY DIFFRACTION100
3.9307-46.39670.16651490.1613085X-RAY DIFFRACTION100

+
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