[English] 日本語
Yorodumi
- PDB-4zm2: Antitoxin Phd from phage P1 in complex with its operator DNA inve... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zm2
TitleAntitoxin Phd from phage P1 in complex with its operator DNA inverted repeat in a monoclinic space group
Components
  • Antitoxin phd
  • DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')
  • DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
KeywordsTRANSCRIPTION / transcription factor / toxin-antitoxin / DNA binding / intrinsic disorder / conditional cooperativity / protein-DNA complex
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
DNA / DNA (> 10) / Antitoxin phd
Similarity search - Component
Biological speciesEnterobacteria phage P1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.88 Å
AuthorsGarcia-Pino, A. / Loris, R.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: An intrinsically disordered entropic switch determines allostery in Phd-Doc regulation.
Authors: Garcia-Pino, A. / De Gieter, S. / Talavera, A. / De Greve, H. / Efremov, R.G. / Loris, R.
History
DepositionMay 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 29, 2016Group: Database references
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antitoxin phd
B: Antitoxin phd
C: Antitoxin phd
D: Antitoxin phd
E: DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
F: DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')
G: DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
H: DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)49,6928
Polymers49,6928
Non-polymers00
Water00
1
A: Antitoxin phd
B: Antitoxin phd
G: DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
H: DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,8464
Polymers24,8464
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-27 kcal/mol
Surface area10100 Å2
MethodPISA
2
C: Antitoxin phd
D: Antitoxin phd
E: DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
F: DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)24,8464
Polymers24,8464
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-26 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.870, 56.580, 74.840
Angle α, β, γ (deg.)90.00, 111.47, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Antitoxin phd / Addiction protein pdh / Prevent host death protein


Mass: 8143.076 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P1 (virus) / Gene: phd / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q06253
#2: DNA chain DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')


Mass: 4270.790 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage P1 (virus)
#3: DNA chain DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')


Mass: 4288.817 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage P1 (virus)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35% 1,4-Dioxane and 200 mM NaCl, 100 mM Tris pH 7.5
PH range: 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.88→43.9 Å / Num. obs: 4674 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 101.35 Å2 / Net I/σ(I): 4.63
Reflection shellResolution: 3.88→4.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.55

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.88→43.92 Å / Cor.coef. Fo:Fc: 0.8138 / Cor.coef. Fo:Fc free: 0.9067 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.819
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 234 5.01 %RANDOM
Rwork0.2615 ---
obs0.262 4674 95.39 %-
Displacement parametersBiso mean: 111.88 Å2
Baniso -1Baniso -2Baniso -3
1-26.8738 Å20 Å29.037 Å2
2--60.383 Å20 Å2
3----87.2568 Å2
Refine analyzeLuzzati coordinate error obs: 1.018 Å
Refinement stepCycle: LAST / Resolution: 3.88→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 1136 0 0 2809
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0152957HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.454224HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d886SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes304HARMONIC5
X-RAY DIFFRACTIONt_it2957HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.39
X-RAY DIFFRACTIONt_other_torsion28.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion402SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3147SEMIHARMONIC4
LS refinement shellResolution: 3.88→4.34 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3192 59 4.98 %
Rwork0.2639 1125 -
all0.2667 1184 -
obs--95.39 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5002-4.4375-1.33841.6-4.62066.6552-0.057-0.846-0.8985-0.4530.66460.11430.4478-0.1347-0.6075-0.4149-0.1528-0.0762-0.04890.26650.64125.045427.39116.397
20.78222.57391.25591.5356-2.40929.2910.79540.1992-0.25620.00580.36641.1719-0.52670.7138-1.16180.10440.04640.10470.24250.0782-0.10776.352833.80778.1088
32.1301-1.4646-3.18193.9078-6.83092.42130.11380.58550.15650.93150.40630.0675-0.37230.0089-0.52010.0931-0.0157-0.05010.0933-0.10180.333127.6311-5.47017.6822
4-0.20652.2642-0.288403.17637.6494-0.11610.3136-0.01770.24880.26920.61550.12570.0351-0.15310.03620.0303-0.05380.00040.03680.274826.4856-11.43235.386
5-0.9318-3.32351.00143.529-3.3160.9318-0.54680.87080.7396-1.1941.08850.06180.86360.7598-0.54170.2851-0.19270.3134-0.059-0.34040.503832.9102-6.2744-14.0096
63.0807-4.0991-4.68374.35124.64263.90160.2505-0.66130.1648-1.10890.2998-0.1544-0.82790.017-0.5503-0.1262-0.1171-0.0941-0.2021-0.12510.647532.1882-3.4245-13.1081
70.799-0.9573-0.8270-6.63139.8080.6583-0.5212-0.5648-1.41140.25780.61460.4707-1.3746-0.9161-0.152-0.3941-0.4276-0.23140.17160.3892-0.135929.0364-14.3172
89.7105-2.31632.67280.0429-7.16590.60030.071-0.152-0.6683-1.2804-0.25540.66610.61470.52140.18440.4643-0.09550.0176-0.3413-0.05250.45041.20926.2907-13.3134
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }

+
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