[English] 日本語
Yorodumi
- PDB-3hry: Crystal structure of PHD in a trigonal space group and partially ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hry
TitleCrystal structure of PHD in a trigonal space group and partially disordered
ComponentsPrevent host death protein
KeywordsANTITOXIN / Phd / Prevent Host Death / intrinsic disorder / DOC
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
Antitoxin phd / Antitoxin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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


Theoretical massNumber of molelcules
Total (without water)24,4293
Polymers24,4293
Non-polymers00
Water75742
1
A: Prevent host death protein
B: Prevent host death protein


Theoretical massNumber of molelcules
Total (without water)16,2862
Polymers16,2862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-13.7 kcal/mol
Surface area7410 Å2
MethodPISA
2
C: Prevent host death protein

C: Prevent host death protein


Theoretical massNumber of molelcules
Total (without water)16,2862
Polymers16,2862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area1620 Å2
ΔGint-9.4 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.951, 71.951, 68.007
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Prevent host death protein / Phd protein


Mass: 8143.076 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: phd, Phd, IPF_68 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q79A04, UniProt: Q06253*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 8000, 8% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
Reflection twinOperator: -k,h+k,l / Fraction: 0.444
ReflectionResolution: 2.25→11.81 Å / Num. all: 9720 / Num. obs: 9720 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 43.2 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.9
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 6.48 / Num. unique all: 471 / Rsym value: 0.248 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
MSCubedata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DD7

3dd7


Resolution: 2.25→11.81 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2563 471 4.85 %
Rwork0.192 --
all0.1948 9720 -
obs0.1948 9720 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.352 Å2 / ksol: 0.29 e/Å3
Refinement stepCycle: LAST / Resolution: 2.25→11.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1133 0 0 42 1175
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_deg1.597
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.25-2.42250.3497970.30331685
2.4225-2.66370.35791020.29991837
2.6637-3.04340.2519800.27221878
3.0434-3.81280.2696880.20231907
3.8128-11.810.2162940.13211952

+
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://pdbjlvh1.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