[English] 日本語
Yorodumi
- PDB-5l8p: Thermolysin in complex with JC114 (PEG400 cryo protectant) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l8p
TitleThermolysin in complex with JC114 (PEG400 cryo protectant)
ComponentsThermolysin
KeywordsHYDROLASE / METALLOPROTEASE / HYDROLASE INHIBITOR COMPLEX
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
Chem-6MG / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å
AuthorsKrimmer, S.G. / Cramer, J. / Heine, A. / Klebe, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council268145-DrugProfilBind Germany
CitationJournal: J. Med. Chem. / Year: 2016
Title: Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands.
Authors: Krimmer, S.G. / Cramer, J. / Betz, M. / Fridh, V. / Karlsson, R. / Heine, A. / Klebe, G.
History
DepositionJun 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Thermolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1989
Polymers34,3601
Non-polymers8388
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-45 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.596, 92.596, 130.427
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
11E-790-

HOH

21E-805-

HOH

-
Components

-
Protein , 1 types, 1 molecules E

#1: Protein Thermolysin / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

-
Non-polymers , 5 types, 431 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-6MG / N~2~-[(R)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-N-[(2S)-2,3,3-trimethylbutyl]-L-leucinamide


Mass: 455.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H38N3O5P
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 MM TRIS/HCL, 1.9 M CSCL, 50% DMSO

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2014
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 83387 / % possible obs: 99.7 % / Redundancy: 12.7 % / Rsym value: 0.062 / Net I/σ(I): 27.6
Reflection shellResolution: 1.29→1.37 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 5.48 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8TLN

8tln


Resolution: 1.29→40.095 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 9.23
RfactorNum. reflection% reflection
Rfree0.1329 4170 5 %
Rwork0.1065 --
obs0.1078 83386 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.29→40.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 44 423 2885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092627
X-RAY DIFFRACTIONf_angle_d1.1843598
X-RAY DIFFRACTIONf_dihedral_angle_d21.648921
X-RAY DIFFRACTIONf_chiral_restr0.083379
X-RAY DIFFRACTIONf_plane_restr0.007475
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2878-1.30250.19521270.14632409X-RAY DIFFRACTION92
1.3025-1.31780.16531370.12832611X-RAY DIFFRACTION100
1.3178-1.33390.16251370.11722587X-RAY DIFFRACTION100
1.3339-1.35080.16651360.11452594X-RAY DIFFRACTION100
1.3508-1.36850.13811390.10982634X-RAY DIFFRACTION100
1.3685-1.38730.14891360.10252594X-RAY DIFFRACTION100
1.3873-1.40710.14881380.1032618X-RAY DIFFRACTION100
1.4071-1.42810.121370.09692597X-RAY DIFFRACTION100
1.4281-1.45040.13561370.09492603X-RAY DIFFRACTION100
1.4504-1.47420.1241370.09172615X-RAY DIFFRACTION100
1.4742-1.49960.10911390.08652628X-RAY DIFFRACTION100
1.4996-1.52690.10861370.08592600X-RAY DIFFRACTION100
1.5269-1.55630.11221370.0812621X-RAY DIFFRACTION100
1.5563-1.5880.08911390.07952628X-RAY DIFFRACTION100
1.588-1.62260.10611380.08272623X-RAY DIFFRACTION100
1.6226-1.66030.11661380.0842619X-RAY DIFFRACTION100
1.6603-1.70180.11651380.08622637X-RAY DIFFRACTION100
1.7018-1.74780.13171390.09022639X-RAY DIFFRACTION100
1.7478-1.79930.10541390.08632626X-RAY DIFFRACTION100
1.7993-1.85740.12741390.09442651X-RAY DIFFRACTION100
1.8574-1.92370.12711390.09672642X-RAY DIFFRACTION100
1.9237-2.00080.12851400.09712648X-RAY DIFFRACTION100
2.0008-2.09180.111390.09932645X-RAY DIFFRACTION100
2.0918-2.20210.10811400.09892673X-RAY DIFFRACTION100
2.2021-2.340.11161410.0952661X-RAY DIFFRACTION100
2.34-2.52070.12091410.10012694X-RAY DIFFRACTION100
2.5207-2.77430.13361420.10812698X-RAY DIFFRACTION100
2.7743-3.17560.1471430.11552721X-RAY DIFFRACTION100
3.1756-4.00040.15881460.12582763X-RAY DIFFRACTION100
4.0004-40.11470.16081550.14342937X-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