[English] 日本語
Yorodumi
- PDB-4z5d: HipB-O4 21mer complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z5d
TitleHipB-O4 21mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')
KeywordsTranscription/DNA / HTH motif / Transcription repressor / HipA sequestering / Transcription-DNA complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / DNA-binding transcription repressor activity / core promoter sequence-specific DNA binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / protein homodimerization activity
Similarity search - Function
Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Antitoxin HipB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMin, J. / Brennan, R.G. / Schumacher, M.A.
CitationJournal: To be published
Title: Molecular mechanism on hipBA gene regulation.
Authors: Min, J. / Wang, A. / Brennan, R.G. / Schumacher, M.A.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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: Antitoxin HipB
B: Antitoxin HipB
C: DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*A)-3')


Theoretical massNumber of molelcules
Total (without water)28,6844
Polymers28,6844
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-56 kcal/mol
Surface area12620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.604, 108.604, 59.189
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-117-

HOH

-
Components

#1: Protein Antitoxin HipB


Mass: 8060.239 Da / Num. of mol.: 2 / Fragment: UNP residues 4-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hipB, b1508, JW1501 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS-T1 / References: UniProt: P23873
#2: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3') / Operator 4 of hiBA operon / top strand


Mass: 6438.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*A)-3') / Operator 4 of hiBA operon / bottom strand


Mass: 6124.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.02M MgCl2, 0.05M sodium cacodylate trihydrate, pH 6.0, 5~30% 2-propanol, 0.001M Spermine

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 4, 2013
RadiationMonochromator: Rigaku Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 22157 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.048 / Χ2: 1.05 / Net I/av σ(I): 44.633 / Net I/σ(I): 15.8 / Num. measured all: 157548
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.194.30.60210920.831199.2
2.19-2.235.50.53610790.8141100
2.23-2.276.30.51511010.8331100
2.27-2.3270.46610990.8951100
2.32-2.377.20.41711070.8781100
2.37-2.427.40.32110760.8721100
2.42-2.487.40.25611130.8751100
2.48-2.557.50.20710850.8941100
2.55-2.627.50.18510930.9041100
2.62-2.717.50.1711150.9071100
2.71-2.817.50.1410980.9581100
2.81-2.927.50.10710860.971100
2.92-3.057.50.0811071.0171100
3.05-3.217.60.05111061.061100
3.21-3.417.50.03511251.2231100
3.41-3.687.50.0310961.2751100
3.68-4.057.50.02611201.425199.9
4.05-4.637.40.02211351.493199.9
4.63-5.837.40.02211311.2991100
5.83-5070.01611931.294199.9

-
Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
HKL-3000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Z52

4z52
PDB Unreleased entry


Resolution: 2.15→47.027 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8872 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 18.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1828 1984 10.04 %
Rwork0.1789 17783 -
obs0.1793 19767 89.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.57 Å2 / Biso mean: 26.0159 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: final / Resolution: 2.15→47.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1128 833 0 270 2231
Biso mean--0 33.62 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122076
X-RAY DIFFRACTIONf_angle_d1.1862977
X-RAY DIFFRACTIONf_chiral_restr0.094344
X-RAY DIFFRACTIONf_plane_restr0.006235
X-RAY DIFFRACTIONf_dihedral_angle_d23.396832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20520.255430.187840945229
2.2052-2.26490.22371160.2081049116575
2.2649-2.33150.25891380.21011228136688
2.3315-2.40680.20551450.21011298144392
2.4068-2.49280.21811440.20381289143393
2.4928-2.59260.23871510.20011349150095
2.5926-2.71050.21221570.20241347150495
2.7105-2.85340.21741550.20581353150896
2.8534-3.03220.20981470.20291351149896
3.0322-3.26620.17221500.17581384153497
3.2662-3.59480.15411540.15681398155298
3.5948-4.11480.13781560.15241427158399
4.1148-5.18310.14081650.15121418158399
5.1831-47.03810.17541630.16871483164699

+
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