[English] 日本語
Yorodumi
- PDB-1s4b: Crystal structure of human thimet oligopeptidase. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s4b
TitleCrystal structure of human thimet oligopeptidase.
ComponentsThimet oligopeptidase
KeywordsHYDROLASE / Zinc metallopeptidase domain
Function / homology
Function and homology information


thimet oligopeptidase / peptide metabolic process / mitochondrial intermembrane space / metalloendopeptidase activity / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / proteolysis / metal ion binding / cytosol
Similarity search - Function
Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Neurolysin; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) ...Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Neurolysin; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thimet oligopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRay, K. / Hines, C.S. / Coll-Rodriguez, J. / Rodgers, D.W.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization
Authors: Ray, K. / Hines, C.S. / Coll-Rodriguez, J. / Rodgers, D.W.
#1: Journal: Protein Sci. / Year: 2002
Title: Mapping sequence differences between thimet oligopeptidase and neurolysin indicates key residues in substrate recognition
Authors: Ray, K. / Hines, C.S. / Rodgers, D.W.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of neurolysin reveals a deep channel that limits substrate access
Authors: Brown, C.K. / Madauss, K. / Lian, W. / Beck, M.R. / Tolbert, W.D. / Rodgers, D.W.
History
DepositionJan 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: Thimet oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5752
Polymers77,5101
Non-polymers651
Water8,539474
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.167, 99.104, 105.505
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a monomer

-
Components

#1: Protein Thimet oligopeptidase / / Endopeptidase 24.15 / MP78


Mass: 77509.961 Da / Num. of mol.: 1 / Mutation: C246S, C253S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOP1 / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3RP / References: UniProt: P52888, thimet oligopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, magnesium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.949 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2002
RadiationMonochromator: Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.949 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 55357 / Num. obs: 55080 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -4 / Biso Wilson estimate: 12.4 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 99.2

-
Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→28 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3019465.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5588 10.1 %RANDOM
Rwork0.201 ---
all0.204 55080 --
obs0.201 55080 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.5102 Å2 / ksol: 0.363661 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.39 Å20 Å20 Å2
2--2.8 Å20 Å2
3---0.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 1 474 5779
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.052
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.632.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 882 9.8 %
Rwork0.224 8109 -
obs--98.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

+
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