[English] 日本語
Yorodumi
- PDB-4z59: HipB-O4 20mer complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z59
TitleHipB-O4 20mer complex
Components
  • Antitoxin HipB
  • DNA (5'-D(*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: 2.3 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: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)14,1942
Polymers14,1942
Non-polymers00
Water2,558142
1
A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')

A: Antitoxin HipB
B: DNA (5'-D(*TP*TP*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)28,3884
Polymers28,3884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area7140 Å2
ΔGint-53 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.370, 127.370, 127.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11B-136-

HOH

-
Components

#1: Protein Antitoxin HipB


Mass: 8060.239 Da / Num. of mol.: 1 / 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*AP*TP*CP*CP*GP*CP*GP*AP*TP*CP*GP*CP*GP*GP*AP*TP*AP*A)-3') / Operator 4 of hiBA operon


Mass: 6133.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 1 M sodium citrate

-
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 7, 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: 2.3→50 Å / Num. obs: 16312 / % possible obs: 100 % / Redundancy: 19.1 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.009 / Net I/av σ(I): 43.152 / Net I/σ(I): 11.5 / Num. measured all: 312178
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3416.40.7557960.7221100
2.34-2.3816.50.7967940.7451100
2.38-2.4316.60.6027890.757199.9
2.43-2.4816.40.5998000.7981100
2.48-2.5316.40.4527850.8071100
2.53-2.5916.50.3988010.8481100
2.59-2.6616.70.3937970.871100
2.66-2.7317.50.3287940.865199.7
2.73-2.8118.10.2687940.9131100
2.81-2.918.80.2328120.945199.9
2.9-319.90.1918121.0061100
3-3.1220.80.1438091.0131100
3.12-3.2621.60.0958001.1241100
3.26-3.4421.80.0728091.2041100
3.44-3.65220.0598181.2241100
3.65-3.93220.0478281.1891100
3.93-4.3321.70.0398321.2441100
4.33-4.9521.70.0368291.2341100
4.95-6.2421.30.0368661.0831100
6.24-5019.30.0259471.0941100

-
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: 2.3→45.032 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8997 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 15.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 1451 10 %
Rwork0.1525 13060 -
obs0.1555 14511 89.16 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.74 Å2 / Biso mean: 23.5411 Å2 / Biso min: 4.18 Å2
Refinement stepCycle: final / Resolution: 2.3→45.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 407 0 142 1114
Biso mean--0 35.8 -
Num. residues----91
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011038
X-RAY DIFFRACTIONf_angle_d1.5621489
X-RAY DIFFRACTIONf_chiral_restr0.077171
X-RAY DIFFRACTIONf_plane_restr0.006121
X-RAY DIFFRACTIONf_dihedral_angle_d23.095416
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.38250.24631160.19481042115873
2.3825-2.47790.27331280.19521153128181
2.4779-2.59060.23991340.18231206134085
2.5906-2.72720.21551380.18051242138087
2.7272-2.8980.18021450.17911300144590
2.898-3.12180.2171500.17081351150193
3.1218-3.43580.15271500.13591349149993
3.4358-3.93270.16081550.12341405156095
3.9327-4.95380.13421600.11471431159196
4.9538-45.04070.17151750.1621581175698
Refinement TLS params.Method: refined / Origin x: 16.9301 Å / Origin y: 42.6362 Å / Origin z: 14.7597 Å
111213212223313233
T0.0513 Å20.0344 Å20.0061 Å2-0.0491 Å2-0.0005 Å2--0.0764 Å2
L0.0239 °2-0.0017 °20.0107 °2-0.0053 °2-0.0036 °2--0.0142 °2
S-0.0161 Å °-0.0335 Å °0.0601 Å °0.0099 Å °0.0076 Å °-0.0264 Å °-0.012 Å °0.0003 Å °-0.0215 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )A4 - 74
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )A101 - 184
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )B101 - 157
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 4:74 OR RESID 101:184 ) ) OR ( CHAIN B AND ( RESID 101:157 OR RESID 1:20 ) )B1 - 20

+
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