[English] 日本語
Yorodumi
- PDB-5l20: Crystal Structure of a Clostripain (BT_0727) from Bacteroides the... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l20
TitleCrystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK
Components
  • (Clostripain-related protein) x 2
  • Peptide Inhibitor BTN-VLTK-AOMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Clostripain / peptidase / microbiome / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homologyPeptidase C11, clostripain / Clostripain family / Prokaryotic membrane lipoprotein lipid attachment site profile. / Peptide Inhibitor BTN-VLTK-AOMK / Clostripain-related protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsWolan, D.W. / Roncase, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)3U54GM094586-03S1 United States
CitationJournal: To be published
Title: Crystal Structure of a Clostripain (BT_0727) from Bacteroides thetaiotaomicron ATCC 29148 in Complex with Peptide Inhibitor BTN-VLTK-AOMK
Authors: Wolan, D.W. / Roncase, E.J.
History
DepositionJul 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Clostripain-related protein
B: Clostripain-related protein
C: Peptide Inhibitor BTN-VLTK-AOMK


Theoretical massNumber of molelcules
Total (without water)43,1073
Polymers43,1073
Non-polymers00
Water7,945441
1
A: Clostripain-related protein
C: Peptide Inhibitor BTN-VLTK-AOMK


Theoretical massNumber of molelcules
Total (without water)17,1402
Polymers17,1402
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Clostripain-related protein


Theoretical massNumber of molelcules
Total (without water)25,9671
Polymers25,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.207, 102.885, 84.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-745-

HOH

21B-781-

HOH

-
Components

#1: Protein Clostripain-related protein


Mass: 16455.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0727 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8
#2: Protein Clostripain-related protein


Mass: 25966.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0727 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8A9T8
#3: Protein/peptide Peptide Inhibitor BTN-VLTK-AOMK


Type: Peptide-like / Class: Inhibitor / Mass: 683.903 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Peptide Inhibitor BTN-VLTK-AOMK
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsthe protein is physically cleaved after Arginine 172

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M Na Citrate, 30% PEG 6000, 2M LiCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.45→43.9 Å / Num. obs: 54597 / % possible obs: 88.95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 13.44 Å2 / CC1/2: 0.957 / Rmerge(I) obs: 0.087 / Rsym value: 0.075 / Net I/σ(I): 21.8
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.9 / CC1/2: 0.774 / % possible all: 44

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
RefinementResolution: 1.45→43.9 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.56
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2729 5 %random selection
Rwork0.1498 ---
obs0.1513 54597 88.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: LAST / Resolution: 1.45→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 441 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112804
X-RAY DIFFRACTIONf_angle_d1.2993826
X-RAY DIFFRACTIONf_dihedral_angle_d11.6991000
X-RAY DIFFRACTIONf_chiral_restr0.055434
X-RAY DIFFRACTIONf_plane_restr0.007483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4479-1.47420.2794700.24461341X-RAY DIFFRACTION44
1.4742-1.50260.2347840.22331636X-RAY DIFFRACTION54
1.5026-1.53320.2184900.2071932X-RAY DIFFRACTION63
1.5332-1.56660.21351340.18032270X-RAY DIFFRACTION75
1.5666-1.6030.20021520.17792740X-RAY DIFFRACTION91
1.603-1.64310.20371630.1732942X-RAY DIFFRACTION97
1.6431-1.68750.20561570.16742945X-RAY DIFFRACTION97
1.6875-1.73720.21031670.16512929X-RAY DIFFRACTION97
1.7372-1.79330.18841810.16412941X-RAY DIFFRACTION97
1.7933-1.85740.16771380.16122899X-RAY DIFFRACTION95
1.8574-1.93170.21871460.15913003X-RAY DIFFRACTION98
1.9317-2.01960.18741480.15252988X-RAY DIFFRACTION98
2.0196-2.12610.16641710.14222987X-RAY DIFFRACTION98
2.1261-2.25930.18791500.14132944X-RAY DIFFRACTION96
2.2593-2.43380.17361690.14992990X-RAY DIFFRACTION98
2.4338-2.67870.17671390.14953066X-RAY DIFFRACTION99
2.6787-3.06620.15311450.14893010X-RAY DIFFRACTION97
3.0662-3.86270.16911570.13063110X-RAY DIFFRACTION99
3.8627-43.91620.16371680.13623195X-RAY DIFFRACTION98

+
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