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- PDB-2cax: STRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX RE... -

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Basic information

Entry
Database: PDB / ID: 2cax
TitleSTRUCTURAL BASIS FOR COOPERATIVE BINDING OF RIBBON-HELIX-HELIX REPRESSOR OMEGA TO MUTATED DIRECT DNA HEPTAD REPEATS
Components
  • 5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*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*G)-3'
  • 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3'
  • 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3'
  • ORF OMEGA
KeywordsTRANSCRIPTIONAL REPRESSOR / INC18 FAMILY OF PLASMIDS / RHH / METJ/ARC SUPERFAMILY / COOPERATIVE DNA BINDING / DNA HEPTAD 5'- A/T ATCAC A/T -3' / PLASMID MAINTENANCE / 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 / OTHER / Resolution: 2.9 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
DepositionDec 23, 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 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
G: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3'
H: 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3'
U: 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3'
Y: 5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)46,0328
Polymers46,0328
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-52 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.957, 44.655, 76.136
Angle α, β, γ (deg.)90.00, 109.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.83355, -0.47475, 0.28251), (-0.4963, 0.41889, -0.76041), (-0.4963, 0.41889, -0.76041)109.31153, 53.77659, 30.05986
2given(-0.81163, -0.496, -0.30861), (-0.56113, 0.51507, 0.64794), (-0.16243, 0.69906, -0.69637)95.90993, 23.00034, 23.84766
3given(0.90651, 0.36242, -0.21656), (0.26275, -0.08279, 0.9613), (0.33047, -0.92833, -0.17028)23.70254, -1.66232, 21.63968
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 ANGSTROMS**2. THE INTERFACEBETWEEN THE PROTEIN DIMER (CHAIN A, B OR CHAINS C, D)IS 1809 ANGSTROMS**2.

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Components

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DNA chain , 4 types, 4 molecules GHUY

#2: DNA chain 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*AP *TP*CP*AP*CP*AP*AP*G)-3'


Mass: 5197.428 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*GP*TP*GP*AP*TP*TP*TP*GP *TP*GP*AP*TP*TP*CP*G)-3'


Mass: 5254.402 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IN INC18 FAMILY PLASMIDS, DIRECT REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR
Source: (synth.) synthetic construct
#4: DNA chain 5'-D(*GP*AP*AP*TP*CP*AP*CP*AP*AP*GP *TP*CP*AP*CP*AP*AP*GP*C)-3'


Mass: 5502.609 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain 5'-D(*CP*TP*TP*GP*TP*GP*AP*CP*TP*TP *GP*TP*GP*AP*TP*TP*CP*G)-3'


Mass: 5528.573 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: IN INC18 FAMILY PLASMIDS, DIRECT REPEATS OCCUR IN PROMOTER REGIONS PRECEDING GENES CONTROLLED BY OMEGA TRANSCRIPTIONAL REPRESSOR
Source: (synth.) synthetic construct

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Protein / Non-polymers , 2 types, 46 molecules ABCD

#1: Protein
ORF OMEGA / ORF OMEGA TRANSCRIPTIONAL REPRESSOR


Mass: 6137.223 Da / Num. of mol.: 4 / Fragment: RIBBON-HELIX-HELIX DOMAIN, RESIDUES 20-71
Source method: isolated from a genetically manipulated source
Details: 19 N-TERMINAL RESIDUES DELETED, NEW N- TERMINAL RESIDUE MET19 IS A CLONING ARTEFACT
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria)
Description: OMEGA TRANSCRIPTIONAL REPRSSSOR 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details19 N-TERMINAL RESIDUES TRUNCATED, NEW MET19 IS A CLONING ARTIFACT

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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: 4.03 Å3/Da / Density % sol: 69.27 % / Description: STRUCTURE IS ISOMORPHOUS TO PDB ENTRY 2BNW
Crystal growpH: 7.5
Details: 150 MM NA/KPO4, PH 7.0, 2.4 M 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: 0.91
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 14144 / % possible obs: 88.6 % / Observed criterion σ(I): 2.5 / Redundancy: 2.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→2.97 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.5 / % possible all: 68.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 20.726 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.43 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 999 7.1 %RANDOM
Rwork0.208 ---
obs0.21 13145 88.6 %-
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: 38.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å23.14 Å2
2--0.13 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1643 1440 0 42 3125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213271
X-RAY DIFFRACTIONr_bond_other_d0.0020.022288
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.5244697
X-RAY DIFFRACTIONr_angle_other_deg0.76635466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.865199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89324.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88915359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8561512
X-RAY DIFFRACTIONr_chiral_restr0.0560.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022511
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.2050.2745
X-RAY DIFFRACTIONr_nbd_other0.2110.22605
X-RAY DIFFRACTIONr_nbtor_refined0.2090.21412
X-RAY DIFFRACTIONr_nbtor_other0.0870.21472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2150.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7471.51312
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84421625
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.13433125
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9484.53072
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: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.32 51
Rwork0.287 758
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)
11.6181.2948-1.05911.6558-0.04652.91720.06380.16630.16090.14910.08380.3653-0.3841-0.2491-0.1476-0.05410.08120.0277-0.06350.0522-0.13044933.89110.658
22.55610.6265-1.74681.5933-1.35843.1390.0060.15760.12010.08870.1663-0.1024-0.25020.2218-0.1723-0.08380.03070.0018-0.12590.0011-0.101955.35935.3259.453
31.55251.5194-1.13872.2441-0.98083.97390.2541-0.00470.19940.4796-0.0984-0.0208-0.0462-0.1944-0.15570.01710.07250.0342-0.12380.0131-0.115934.02819.51430.717
42.96921.3462-0.04386.24422.5423.91010.32490.1678-0.00050.2468-0.11050.54750.0116-0.5643-0.2144-0.06290.0127-0.003-0.13740.0291-0.185728.92616.19930.91
510.73433.2759-0.17982.5820.13491.9957-0.08530.1068-0.32-0.02270.1283-0.09270.2012-0.2023-0.0431-0.07180.0728-0.0178-0.175-0.0023-0.186443.47816.63915.585
67.95462.249-1.36692.7869-0.07451.45780.09990.2619-0.4555-0.0591-0.0148-0.1930.1243-0.0615-0.0851-0.09630.1021-0.0479-0.11760.0065-0.23644.82616.75516.914
718.44263.8411-3.24251.5672-0.72891.1929-0.2888-0.0367-0.53780.00870.2736-0.0912-0.11860.35210.0152-0.6739-0.087-0.13520.5243-0.0890.345798.6829.10313.254
810.7771.10770.41450.16590.06750.02780.03920.04240.5053-0.1405-0.0595-0.04310.14810.39850.0203-0.5539-0.1323-0.03650.65490.02170.543596.1630.83412.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 69
2X-RAY DIFFRACTION2B24 - 69
3X-RAY DIFFRACTION3C24 - 69
4X-RAY DIFFRACTION4D25 - 69
5X-RAY DIFFRACTION5U1 - 18
6X-RAY DIFFRACTION6Y21 - 38
7X-RAY DIFFRACTION7G2 - 18
8X-RAY DIFFRACTION8H22 - 38

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