[English] 日本語
Yorodumi
- PDB-6pdq: Ancestral Effector Caspase 3/6/7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pdq
TitleAncestral Effector Caspase 3/6/7
Components
  • (Ancestral Effector Caspase-3/6/7) x 2
  • Ac-DEVD inhibitor
KeywordsAPOPTOSIS / Ancestral Effector Caspase / protease / ancestral protein reconstruction
Function / homologyCaspase-like / Rossmann fold - #1460 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsClark, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127654 United States
CitationJournal: Biochem.J. / Year: 2019
Title: Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity.
Authors: Grinshpon, R.D. / Shrestha, S. / Titus-McQuillan, J. / Hamilton, P.T. / Swartz, P.D. / Clark, A.C.
History
DepositionJun 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ancestral Effector Caspase-3/6/7
B: Ancestral Effector Caspase-3/6/7
D: Ancestral Effector Caspase-3/6/7
E: Ancestral Effector Caspase-3/6/7
F: Ac-DEVD inhibitor
G: Ac-DEVD inhibitor


Theoretical massNumber of molelcules
Total (without water)54,2696
Polymers54,2696
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-83 kcal/mol
Surface area16570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.169, 78.760, 107.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ancestral Effector Caspase-3/6/7


Mass: 16070.114 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein Ancestral Effector Caspase-3/6/7


Mass: 10561.993 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide Ac-DEVD inhibitor


Mass: 502.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, pH 4.6, 0.1 M sodium acetate trihydrate, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→43.493 Å / Num. obs: 39730 / % possible obs: 99.23 % / Redundancy: 7 % / Net I/σ(I): 8.5
Reflection shellResolution: 1.83→1.89 Å / Num. unique obs: 3741

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→43.493 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.31
RfactorNum. reflection% reflection
Rfree0.2339 1993 5.03 %
Rwork0.1914 --
obs0.1935 39627 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.83→43.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 0 179 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063639
X-RAY DIFFRACTIONf_angle_d0.8074910
X-RAY DIFFRACTIONf_dihedral_angle_d7.8742985
X-RAY DIFFRACTIONf_chiral_restr0.051553
X-RAY DIFFRACTIONf_plane_restr0.004633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87580.38181310.29542496X-RAY DIFFRACTION93
1.8758-1.92650.321420.29932699X-RAY DIFFRACTION100
1.9265-1.98320.28311390.24262611X-RAY DIFFRACTION100
1.9832-2.04720.24731400.20792678X-RAY DIFFRACTION100
2.0472-2.12030.27121410.22372659X-RAY DIFFRACTION100
2.1203-2.20520.28241430.19822680X-RAY DIFFRACTION100
2.2052-2.30560.26071420.22572664X-RAY DIFFRACTION100
2.3056-2.42710.25311410.18682677X-RAY DIFFRACTION100
2.4271-2.57920.24151430.1972682X-RAY DIFFRACTION100
2.5792-2.77830.24681440.19912728X-RAY DIFFRACTION100
2.7783-3.05780.25711440.18822710X-RAY DIFFRACTION100
3.0578-3.50010.21541450.18252728X-RAY DIFFRACTION100
3.5001-4.40910.18731460.15452752X-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