[English] 日本語
Yorodumi
- PDB-3hs2: Crystal structure of PHD truncated to residue 57 in an orthorhomb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hs2
TitleCrystal structure of PHD truncated to residue 57 in an orthorhombic space group
ComponentsPrevent host death protein
KeywordsANTITOXIN / Prevent Host Death / PHD / intrinsic disorder / Doc / toxin-antitoxin
Function / homology
Function and homology information


toxin sequestering activity / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding
Similarity search - Function
YefM-like domain / Type II toxin-antitoxin system, antitoxin Phd/YefM / Antitoxin Phd_YefM, type II toxin-antitoxin system / YefM-like superfamily / YefM-like fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Allostery and intrinsic disorder mediate transcription regulation by conditional cooperativity.
Authors: Garcia-Pino, A. / Balasubramanian, S. / Wyns, L. / Gazit, E. / De Greve, H. / Magnuson, R.D. / Charlier, D. / van Nuland, N.A. / Loris, R.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Prevent host death protein
B: Prevent host death protein
C: Prevent host death protein
D: Prevent host death protein
E: Prevent host death protein
F: Prevent host death protein
G: Prevent host death protein
H: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,73014
Polymers51,1538
Non-polymers5766
Water1,49583
1
A: Prevent host death protein
B: Prevent host death protein
G: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3755
Polymers19,1823
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-21.1 kcal/mol
Surface area6000 Å2
MethodPISA
2
B: Prevent host death protein
C: Prevent host death protein
D: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4716
Polymers19,1823
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-20.5 kcal/mol
Surface area6180 Å2
MethodPISA
3
D: Prevent host death protein
E: Prevent host death protein
F: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3755
Polymers19,1823
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-19.6 kcal/mol
Surface area5760 Å2
MethodPISA
4
F: Prevent host death protein
G: Prevent host death protein
H: Prevent host death protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4716
Polymers19,1823
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-14.4 kcal/mol
Surface area5640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.001, 122.542, 61.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Prevent host death protein / Phd protein


Mass: 6394.143 Da / Num. of mol.: 8 / Fragment: N-terminal domain: UNP residues 1-58
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: phd / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06253
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 1.96 Å3/Da / Density % sol: 37.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 8000, 0.2M LiSO4, 0.1M Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.2→34.25 Å / Num. all: 20810 / Num. obs: 20810 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 6.87 / Num. unique all: 2025 / Rsym value: 0.321 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HRY

3hry


Resolution: 2.2→34.25 Å / SU ML: 1.74 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2706 1448 7.23 %
Rwork0.2274 --
all0.2305 20810 -
obs0.2305 20810 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.099 Å2 / ksol: 0.379 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 30 83 3317
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_deg0.777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.27870.30051560.2525177995
2.2787-2.36990.29481510.2309181396
2.3699-2.47770.31471350.2367184697
2.4777-2.60830.30951480.2425184397
2.6083-2.77170.29221580.2313186698
2.7717-2.98550.29191320.2287191199
2.9855-3.28580.27781540.2162188599
3.2858-3.76070.24191290.2111193598
3.7607-4.73610.22681390.2053181493
4.7361-34.250.27031460.2441187492

+
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