[English] 日本語
Yorodumi
- PDB-6sbk: THERMOLYSIN IN COMPLEX WITH FRAGMENT J13 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sbk
TitleTHERMOLYSIN IN COMPLEX WITH FRAGMENT J13
ComponentsThermolysin
KeywordsHYDROLASE / THERMOLYSIN / METALLOPROTEASE / FRAGMENT COMPLEX
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / 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 ...: / 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 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine / ISOPROPYL ALCOHOL / (2,5-dimethylpyrazol-3-yl)methylcarbamic acid / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsMagari, F. / Heine, A. / Klebe, G.
CitationJournal: To Be Published
Title: THERMOLYSIN IN COMPLEX WITH FRAGMENT J13
Authors: Magari, F. / Heine, A. / Klebe, G.
History
DepositionJul 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,29713
Polymers34,3601
Non-polymers93712
Water4,864270
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-42 kcal/mol
Surface area12420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.561, 92.561, 129.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11E-708-

HOH

21E-728-

HOH

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

-
Non-polymers , 8 types, 282 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-47J / 1-(1,3-dimethyl-1H-pyrazol-5-yl)methanamine


Mass: 125.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-L4Z / (2,5-dimethylpyrazol-3-yl)methylcarbamic acid


Mass: 169.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→46.28 Å / Num. obs: 54619 / % possible obs: 99.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.999 / Rsym value: 0.062 / Net I/σ(I): 20.24
Reflection shellResolution: 1.48→1.57 Å / Mean I/σ(I) obs: 3.99 / Num. unique obs: 8612 / CC1/2: 0.911 / Rsym value: 0.478 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata scaling
XDSdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.48→46.28 Å / SU ML: 0.1172 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.6511
RfactorNum. reflection% reflection
Rfree0.1692 2731 5 %
Rwork0.1504 --
obs0.1514 54619 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.41 Å2
Refinement stepCycle: LAST / Resolution: 1.48→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2414 0 50 270 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042581
X-RAY DIFFRACTIONf_angle_d0.75033523
X-RAY DIFFRACTIONf_chiral_restr0.0692369
X-RAY DIFFRACTIONf_plane_restr0.0043481
X-RAY DIFFRACTIONf_dihedral_angle_d16.0583895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.510.24171330.20332526X-RAY DIFFRACTION98.01
1.51-1.530.21181310.17942507X-RAY DIFFRACTION98.4
1.53-1.560.18541340.16772542X-RAY DIFFRACTION98.45
1.56-1.590.18761330.15952523X-RAY DIFFRACTION98.55
1.59-1.630.18151340.15222544X-RAY DIFFRACTION98.78
1.63-1.670.18781340.14752539X-RAY DIFFRACTION98.82
1.67-1.710.15541340.14972556X-RAY DIFFRACTION98.93
1.71-1.750.14171340.14562538X-RAY DIFFRACTION99.04
1.75-1.810.1641350.13752577X-RAY DIFFRACTION99.12
1.81-1.860.16331350.14582566X-RAY DIFFRACTION99.37
1.86-1.930.15711360.14382577X-RAY DIFFRACTION99.23
1.93-2.010.19521360.1412582X-RAY DIFFRACTION99.6
2.01-2.10.16761360.13812589X-RAY DIFFRACTION99.56
2.1-2.210.14981370.13732602X-RAY DIFFRACTION99.56
2.21-2.350.15381370.12772599X-RAY DIFFRACTION99.89
2.35-2.530.13071380.13412624X-RAY DIFFRACTION99.89
2.53-2.790.15941400.14042653X-RAY DIFFRACTION99.93
2.79-3.190.17411400.14732670X-RAY DIFFRACTION99.89
3.19-4.020.16711420.1522699X-RAY DIFFRACTION99.86
4.02-46.280.19051520.17862875X-RAY DIFFRACTION99.84
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3324303001420.09597620237040.04365942255340.147388477373-0.04686076326870.1485322527870.0812152768240.0577991670993-0.09106885137120.0287086518277-0.0262504621534-0.0409058810806-0.0265466914518-0.003071919126550.1893083881090.02227789074880.02274536365040.01948569541380.05181643972550.00594745963378-0.003253158348524.893755731331.35193322752.98445943925
20.01788666683890.01092410966930.009181663722980.009544890445170.001488173861170.004475617392250.0100494473140.04106122157260.0418680187658-0.03184762527330.026023804038-0.0196856087493-0.0183988973615-0.007183241410020.007378810519060.09994375190240.01887731934770.01331972503560.134174909808-0.007443883226530.10461950747512.88419083235.1732332805-4.3540065661
30.001293105116-0.000663598078002-0.002418179958810.0130285511450.01278133097830.01133592662830.0224452265282-0.0209172275173-0.0320495835745-0.0288614886961-0.02609219742510.0496521855435-0.0116526593899-0.008648368570777.82817943383E-60.07348714556710.01444343702890.004955716086120.108857870860.01014747095820.08949148318936.1087959171128.9771141168-6.16730160012
40.0106238917558-0.00026758837273-0.007783982586280.00670584226710.005656265032760.005442728479040.0307279929886-0.04894969147470.02942440197420.0216464751026-0.04010287273560.00905259990698-0.0366726428505-0.0836000606215-0.001524957918090.1073612072180.01169460915750.02691540643320.183232475705-0.01624032588640.13668744751.495251887235.27974772635.35267517934
50.006546402752380.003497249259840.00884351171670.01316689852470.01209831917190.0162517890374-0.06088118532320.0001135161427270.0163752360561-0.0444172340408-0.01279414430450.0367260274771-0.111614270237-0.0814350922992-0.004869707284820.1382648809130.0439508174733-0.01997319412690.149288173114-0.00992905426920.162228852124-2.9905256956640.5201891605-12.0983917837
60.03543692859270.01223151819570.03442746792820.0456716339990.003925197078520.04067931625710.0685306309429-0.0211399109085-0.149943182846-0.0731284586518-0.04055573136030.09506845247760.0670879752686-0.1293103420470.004795958860730.107984377265-0.00256794966921-0.002178279593560.156858555579-0.005077384237960.165760782634-1.2906406131722.6135047423-11.1824002755
70.0111271417485-0.00205044559657-0.001555364392190.00271740130236-5.28757463962E-50.001859478407280.04543273618030.0120078000843-0.04656733428120.0088075473393-0.006038808554690.005155978980880.0158676666437-0.1222046943630.007958833206790.109497603312-0.0313228416178-0.02737226759350.176621718189-0.01775617091480.224014657615-8.5221968387119.4975115751-13.0452334956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'E' and (resid 123 through 158 )
3X-RAY DIFFRACTION3chain 'E' and (resid 159 through 180 )
4X-RAY DIFFRACTION4chain 'E' and (resid 181 through 211 )
5X-RAY DIFFRACTION5chain 'E' and (resid 212 through 232 )
6X-RAY DIFFRACTION6chain 'E' and (resid 233 through 296 )
7X-RAY DIFFRACTION7chain 'E' and (resid 297 through 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://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