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Basic information

Entry
Database: PDB / ID: 2bnz
TitleStructural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to inverted DNA heptad repeats
Components
  • 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
  • 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'
  • ORF OMEGA
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / RIBBON-HELIX-HELIX / RHH / METJ/ARC SUPERFAMILY / COOPERATIVE DNA BINDING / INC18 FAMILY
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: 2.6 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 6, 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 1.2Oct 21, 2015Group: Other / Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'
F: 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'
G: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'
H: 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)46,6098
Polymers46,6098
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12840 Å2
ΔGint-104.2 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.991, 42.505, 103.727
Angle α, β, γ (deg.)90.00, 107.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8117, -0.52009, 0.2658), (-0.54328, 0.50522, -0.67052), (0.21444, -0.68867, -0.69264)-27.64397, -14.37253, -10.42639
2given(-0.04934, 0.82837, -0.558), (-0.9933, 0.01774, 0.11418), (0.10448, 0.55989, 0.82195)-23.72695, -9.2767, 23.01543
3given(-0.53771, 0.81906, -0.20002), (0.82827, 0.4688, -0.30691), (-0.15761, -0.33069, -0.93049)-28.82347, 17.26773, 4.42905
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. BUTIS LARGELY UNOBSERVED IN ELECTRON DENSITY MAPS.

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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*GP *TP*GP*AP*TP*TP*AP*GP*C)-3'


Mass: 5548.630 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*CP*TP*AP*AP*TP*CP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Mass: 5481.564 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: INVERTED REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR, PLASMID PSM19035
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.6 Å3/Da / Density % sol: 65.9 %
Crystal growpH: 7.5
Details: 120 MM NA/KPO4, PH 7.2, 2.2 M DINATRIUMMALONATE, PH 7.5, 3 % 2-METHYL-2,4-PENTANDIOL

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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 15, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→35 Å / Num. obs: 18516 / % possible obs: 92.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.1 / % possible all: 72.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BNW

2bnw


Resolution: 2.6→100 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.877 / SU B: 18.753 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.365 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NUCLEOTIDES G5-G16, G18, E18 AND H19-H31 WERE NOT MODELLED DUE TO PATCHY ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.258 944 5.1 %RANDOM
Rwork0.225 ---
obs0.227 17564 92.8 %-
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: 34.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å22.27 Å2
2--0.1 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1613 927 0 45 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212665
X-RAY DIFFRACTIONr_bond_other_d0.0020.022009
X-RAY DIFFRACTIONr_angle_refined_deg1.0442.413765
X-RAY DIFFRACTIONr_angle_other_deg0.72734771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31224.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02615349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.491512
X-RAY DIFFRACTIONr_chiral_restr0.0510.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_nbd_refined0.2080.3616
X-RAY DIFFRACTIONr_nbd_other0.20.32265
X-RAY DIFFRACTIONr_nbtor_refined0.2060.51179
X-RAY DIFFRACTIONr_nbtor_other0.0880.51301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.4164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1810.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.48
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.87821294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05131594
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.55422201
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.03532171
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: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.404 48
Rwork0.366 981
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)
12.42140.0862-0.45180.84840.31861.1087-0.1025-0.0442-0.057-0.00030.05930.01270.03010.03660.0431-0.0533-0.0011-0.0088-0.08340.03170.0287-11.7706-13.0601-2.2275
21.4921-0.1307-0.45711.7929-0.81530.5507-0.1373-0.1088-0.118-0.05150.1765-0.08850.2074-0.0539-0.0392-0.04250.02940.0334-0.04560.01290.0116-9.4437-19.70560.8256
31.7414-0.92440.00543.13710.6821.1969-0.1447-0.2663-0.01440.11310.08430.01680.01710.08760.0604-0.08350.0402-0.0122-0.0381-0.0223-0.0227-32.79932.228512.233
44.77690.05820.02584.21412.62432.3797-0.0378-0.10260.08170.09360.0820.07930.1904-0.006-0.0442-0.09280.02320.0193-0.07590.0192-0.0561-40.1214-0.009111.7257
51.64-1.3528-2.20651.13841.61864.7785-0.0111-0.11780.036-0.00670.0572-0.1418-0.11790.0202-0.046-0.113-0.0104-0.0163-0.0335-0.0138-0.0268-17.55031.94134.6985
62.1353-0.6071-1.49971.47351.62924.381-0.0236-0.13790.0798-0.0230.0852-0.1519-0.07670.17-0.0616-0.09290.0023-0.0114-0.11970.0117-0.0379-18.91192.244.0972
73.4902-1.0287-4.27561.27360.32366.14150.29260.24650.3769-0.41010.047-0.2294-0.14660.1533-0.33960.2096-0.0690.05740.22990.064-0.1959-8.0201-8.1992-19.3437
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 - 17
10X-RAY DIFFRACTION6F21 - 36
11X-RAY DIFFRACTION7G2 - 17
12X-RAY DIFFRACTION7H34 - 38

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