[English] 日本語
Yorodumi
- PDB-2bnw: Structural basis for cooperative binding of Ribbon-Helix-Helix Om... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bnw
TitleStructural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats
Components
  • 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
  • 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'
  • ORF OMEGA
KeywordsDNA-BINDING/REGULATORY PROTEIN / DNA-BINDING-REGULATORY PROTEIN COMPLEX / RIBBON-HELIX-HELIX / RHH / METJ/ARC SUPERFAMILY / COOPERATIVE DNA BINDING / INVERTED REPEATS / DNA HEPTAD / INC18 FAMILY / DNA-BINDING REGULATORY PROTEIN
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
Omega transcriptional repressor / Omega Transcriptional Repressor / Met repressor-like / Arc Repressor Mutant / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional repressor
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWeihofen, W.A. / Cicek, A. / Pratto, F. / Alonso, J.C. / Saenger, W.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structures of Omega Repressors Bound to Direct and Inverted DNA Repeats Explain Modulation of Transcription.
Authors: Weihofen, W.A. / Cicek, A. / Pratto, F. / Alonso, J.C. / Saenger, W.
History
DepositionApr 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 29, 2020Group: Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn
Item: _pdbx_database_status.status_code_sf / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Dec 13, 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: ORF OMEGA
B: ORF OMEGA
C: ORF OMEGA
D: ORF OMEGA
E: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'
F: 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
G: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'
H: 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)46,6098
Polymers46,6098
Non-polymers00
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)219.426, 44.631, 75.960
Angle α, β, γ (deg.)90.00, 108.80, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.83429, -0.4805, 0.27034), (-0.49429, 0.43467, -0.75282), (0.24422, -0.76169, -0.60015)109.69965, 53.00224, 29.66882
2given(0.91555, 0.27137, 0.29685), (0.32963, -0.0834, -0.94042), (-0.23045, 0.95885, -0.16581)-28.76051, 13.07345, 11.35475
3given(-0.81481, -0.56406, -0.13391), (-0.46838, 0.50439, 0.7254), (-0.34163, 0.65378, -0.67517)95.1518, 17.72947, 32.99157
DetailsTHE DESIGNATION OF THE QUATERNARY STRUCTURE AS OCTAMERICREFLECTS THE STANDARD PQS CONVENTION FOR DESCRIBINGHETEROGENEOUS ASSEMBLIES. HOWEVER, THE CRYSTALLOGRAPHICASYMMETRIC UNIT ACTUALLY CONTAINS ONE DNA FRAGMENT(COMPRISED OF CHAINS E AND F) WHICH IS BOUND TO TWOPROTEIN DIMERS (CHAINS A, B, C AND D). A FURTHER FREEDNA FRAGMENT (CHAINS G AND H) IS PRESENT IN THE A.U.THE INTERFACE BETWEEN THE TWO PROTEIN DIMERS AND DNAIS 1600 ANGSTROMS**2 AND THE INTERFACE BETWEEN THETWO PROTEIN DIMERS IS 280 ANSGTROMS**2.

-
Components

#1: Protein
ORF OMEGA / OMEGA TRANSCRIPTIONAL REPRESSOR / ORF OMEGA'


Mass: 6137.223 Da / Num. of mol.: 4 / Fragment: RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria)
Description: OMEGA TRANSCRIPTIONAL REPRESSOR IS ENCODED BY PLASMID PSM19035 OF THE INC18 FAMILY OF PLASMIDS
Plasmid: PET28A-DELTA19OMEGA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57468
#2: DNA chain 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*GP*C)-3'


Mass: 5486.610 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS
Source: (synth.) synthetic construct
#3: DNA chain 5'-D(*CP*TP*TP*GP*TP*GP*AP*TP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Mass: 5543.584 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: DIRECT DNA HEPTAD REPEATS OCCUR IN PROMOTERS PRECEEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL EPRESSOR, INC18 FAMILY OF PLASMIDS
Source: (synth.) synthetic construct
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Sequence details19 N-TERMINAL RESIDUES TRUNCATED, NEW N-TERMINAL MET19 IS A CLONING ARTEFACT.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69 %
Crystal growpH: 7
Details: 150 MM NA/KPO4, PH 7.0, 2.4 NA2MALONATE, PH 7.5, 2% AMINOCAPROIC ACID

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 83105 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.7
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3 / % possible all: 81.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IRQ AND 1CMA

1irq

1cma


Resolution: 2.45→43.44 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.188 / SU ML: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CYTOSINES E18 AND G18 WERE ONLY MODELED FOR THE 5'- PHOSPATE AND ATOM C5'
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1044 4.1 %RANDOM
Rwork0.226 ---
obs0.227 24191 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å2-1.1 Å2
2--1.44 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 1440 0 79 3153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213262
X-RAY DIFFRACTIONr_bond_other_d0.0030.022285
X-RAY DIFFRACTIONr_angle_refined_deg1.3852.524686
X-RAY DIFFRACTIONr_angle_other_deg0.79835449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3124.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.07215355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2291512
X-RAY DIFFRACTIONr_chiral_restr0.0530.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_nbd_refined0.2140.3664
X-RAY DIFFRACTIONr_nbd_other0.2030.32576
X-RAY DIFFRACTIONr_nbtor_refined0.2110.51404
X-RAY DIFFRACTIONr_nbtor_other0.0910.51428
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.4215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.329
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1880.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.411
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5851.51305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66321617
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.88233011
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4264.53069
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 58
Rwork0.317 1416
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)
11.96820.0562-1.23460.94890.30631.8611-0.01910.1302-0.00710.08460.1002-0.048-0.03270.0025-0.0811-0.03960.04080.0035-0.12540.0281-0.122853.223131.507311.6711
23.443-1.0444-2.06592.3854-0.64882.026-0.12970.07030.19510.02430.27310.0488-0.0383-0.0639-0.1434-0.06390.0036-0.0009-0.09320.0074-0.129851.029438.08688.1859
30.92940.8157-0.23213.1046-0.45221.60520.0960.06630.0392-0.02530.030.18640.0529-0.1613-0.126-0.02280.0382-0.004-0.0648-0.0011-0.13732.428716.706327.489
42.23551.397-0.97483.36171.35921.98180.01610.01130.101-0.03130.11420.0534-0.0179-0.2027-0.1304-0.02090.03540.0022-0.07760.029-0.109130.791419.01434.8059
54.55411.8683-1.02652.2753-0.50471.3444-0.08520.0781-0.1776-0.08310.0764-0.03080.1195-0.04910.0089-0.0770.0587-0.0286-0.1424-0.014-0.192345.181517.072515.4878
64.00721.2707-0.44091.36980.10711.25030.0460.1273-0.13540.0024-0.0024-0.03940.0028-0.0682-0.0436-0.07540.0502-0.0379-0.13140.0276-0.179745.14316.723416.9562
72.04970.3533-0.1180.0609-0.02030.0068-0.1329-0.13180.07470.01240.0843-0.0766-0.03280.12610.04860.042-0.0191-0.03920.24210.00410.162493.496230.005312.4643
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 50
2X-RAY DIFFRACTION1B24 - 50
3X-RAY DIFFRACTION2A51 - 67
4X-RAY DIFFRACTION2B51 - 67
5X-RAY DIFFRACTION3C24 - 50
6X-RAY DIFFRACTION3D24 - 50
7X-RAY DIFFRACTION4C51 - 67
8X-RAY DIFFRACTION4D51 - 67
9X-RAY DIFFRACTION5E1 - 18
10X-RAY DIFFRACTION6F19 - 36
11X-RAY DIFFRACTION7G2 - 18
12X-RAY DIFFRACTION7H34 - 38

+
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