[English] 日本語
Yorodumi
- PDB-5uua: Tetragonal thermolysin cryocooled to 100 K with 50% xylose as cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5uua
TitleTetragonal thermolysin cryocooled to 100 K with 50% xylose as cryoprotectant
ComponentsThermolysin
KeywordsHYDROLASE / zinc protease / alpha/beta
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
beta-D-xylopyranose / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.60000384919 Å
AuthorsJuers, D.H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order.
Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z.
History
DepositionFeb 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,30723
Polymers34,3601
Non-polymers1,94622
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-363 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.705, 96.705, 106.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

-
Protein / Sugars , 2 types, 9 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)
Gene: npr / Production host: Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#5: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 475 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / 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: 3.63 Å3/Da / Density % sol: 66.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 50 mg/mL in 45% DMSO, 0.5 M ZnC2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Aug 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.6→21.2 Å / Num. obs: 127553 / % possible obs: 100 % / Redundancy: 20.5 % / Biso Wilson estimate: 15.3600259248 Å2 / CC1/2: 0.999 / Net I/σ(I): 29.3
Reflection shellHighest resolution: 1.6 Å / Redundancy: 13.1 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.734 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALAdata scaling
CrysalisProdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.60000384919→21.0355652469 Å / SU ML: 0.145654428223 / Cross valid method: FREE R-VALUE / σ(F): 1.34439842831 / Phase error: 16.0668765575
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.166000093328 3844 3.01431091943 %
Rwork0.144735730355 123681 -
obs0.145369092285 127525 99.9772645311 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.9942011237 Å2
Refinement stepCycle: LAST / Resolution: 1.60000384919→21.0355652469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 94 461 2987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01030274661562732
X-RAY DIFFRACTIONf_angle_d1.078052496753758
X-RAY DIFFRACTIONf_chiral_restr0.061732078158424
X-RAY DIFFRACTIONf_plane_restr0.00705451933052484
X-RAY DIFFRACTIONf_dihedral_angle_d9.845676102881585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62020.2947830000731400.27765881264595X-RAY DIFFRACTION99.9366821444
1.6202-1.64160.2672116047431420.261058335834548X-RAY DIFFRACTION99.9786825837
1.6416-1.6640.3052366158911410.2512905691054614X-RAY DIFFRACTION100
1.664-1.68780.2546014836731420.2342486266614590X-RAY DIFFRACTION100
1.6878-1.7130.2300155264221450.2237430664454551X-RAY DIFFRACTION100
1.713-1.73970.2264839791441430.2151807085054589X-RAY DIFFRACTION100
1.7397-1.76820.1924255094881420.2085979350064575X-RAY DIFFRACTION100
1.7682-1.79870.1962548171461430.1918778158944617X-RAY DIFFRACTION100
1.7987-1.83140.2074580215531400.1811654336564556X-RAY DIFFRACTION100
1.8314-1.86660.1943305162691420.1716266914124583X-RAY DIFFRACTION100
1.8666-1.90470.1711301951271490.1671272414974577X-RAY DIFFRACTION100
1.9047-1.94610.1900668295441420.1548921431224606X-RAY DIFFRACTION100
1.9461-1.99130.1602261208381410.154747099424521X-RAY DIFFRACTION100
1.9913-2.04110.1684271780741450.1515096716424640X-RAY DIFFRACTION100
2.0411-2.09620.1960511141231470.1492107775454553X-RAY DIFFRACTION100
2.0962-2.15780.2078568322141360.1438137292964576X-RAY DIFFRACTION100
2.1578-2.22740.1675235514791430.1347039662944563X-RAY DIFFRACTION100
2.2274-2.30690.1251850068931420.1238575595444610X-RAY DIFFRACTION100
2.3069-2.39920.1287685311311390.1184707256514588X-RAY DIFFRACTION100
2.3992-2.50820.1473599082351440.1235219199294569X-RAY DIFFRACTION100
2.5082-2.64020.1182912194711420.1154682575984579X-RAY DIFFRACTION100
2.6402-2.80530.1145990482911470.1116004623014596X-RAY DIFFRACTION100
2.8053-3.02130.1270780491861370.1173121304114574X-RAY DIFFRACTION100
3.0213-3.32420.1796840356571410.1278826668144585X-RAY DIFFRACTION100
3.3242-3.80280.1266398404341420.1219048981064584X-RAY DIFFRACTION100
3.8028-4.78180.1416377837021440.1111711536424585X-RAY DIFFRACTION100
4.7818-21.03740.2023887390591430.1640944815294557X-RAY DIFFRACTION99.4708994709

+
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