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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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.

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Experimental details

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Experiment

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

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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

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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

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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

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