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- PDB-1rio: Structure of bacteriophage lambda cI-NTD in complex with sigma-re... -

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Basic information

Entry
Database: PDB / ID: 1rio
TitleStructure of bacteriophage lambda cI-NTD in complex with sigma-region4 of Thermus aquaticus bound to DNA
Components
  • (27-MER) x 2
  • Repressor protein CI
  • sigma factor SigA
Keywordstranscription/DNA / HELIX-TURN-HELIX / TRANSCRIPTION ACTIVATION / transcription-DNA COMPLEX
Function / homology
Function and homology information


maintenance of viral latency / latency-replication decision / positive regulation of viral transcription / negative regulation of transcription by competitive promoter binding / sigma factor activity / core promoter sequence-specific DNA binding / DNA-templated transcription initiation / DNA binding / identical protein binding / cytoplasm
Similarity search - Function
: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / 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 ...: / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / 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) / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Lambda repressor-like, DNA-binding domain superfamily / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein cI / RNA polymerase sigma factor SigA
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
Enterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJain, D. / Nickels, B.E. / Sun, L. / Hochschild, A. / Darst, S.A.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of a ternary transcription activation complex.
Authors: Jain, D. / Nickels, B.E. / Sun, L. / Hochschild, A. / Darst, S.A.
History
DepositionNov 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
U: 27-MER
T: 27-MER
H: sigma factor SigA
A: Repressor protein CI
B: Repressor protein CI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7747
Polymers47,6155
Non-polymers1582
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.256, 71.269, 77.199
Angle α, β, γ (deg.)90.00, 91.34, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules UT

#1: DNA chain 27-MER


Mass: 8293.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#2: DNA chain 27-MER


Mass: 8302.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized

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Protein , 2 types, 3 molecules HAB

#3: Protein sigma factor SigA


Mass: 8719.089 Da / Num. of mol.: 1 / Fragment: Sigma region 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: pAO6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9EZJ8
#4: Protein Repressor protein CI


Mass: 11150.298 Da / Num. of mol.: 2 / Fragment: cI-N-terminus domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Gene: CI / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03034

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Non-polymers , 3 types, 178 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growTemperature: 295 K / pH: 4.6
Details: MPD, Sodium Acetate, calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 4.60
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2Sodium Acetate11
3calcium chloride11
4H2O11
5Sodium Acetate12
6calcium chloride12
7H2O12
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
118 %1reservoir
220 mM1reservoirCaCl2
30.1 Msodium acetate1reservoirpH4.6
425 mg/mlprotein1drop
510 mMHEPES1droppH7.5
6150 mM1dropNaCl
70.1 mMEDTA1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.97946 / Wavelength: 0.97938,0.97927,0.9648
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2002
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979461
20.979381
30.979271
40.96481
ReflectionResolution: 2.25→30 Å / Num. obs: 22889

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.884 / SU ML: 0.217 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.231
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1095 4.8 %RANDOM
Rwork0.216 ---
obs0.218 21761 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2000 1101 9 176 3286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213256
X-RAY DIFFRACTIONr_bond_other_d0.0010.022386
X-RAY DIFFRACTIONr_angle_refined_deg2.3532.3944605
X-RAY DIFFRACTIONr_angle_other_deg1.14335664
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7453248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58715402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1260.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022774
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02387
X-RAY DIFFRACTIONr_nbd_refined0.2580.3753
X-RAY DIFFRACTIONr_nbd_other0.250.32579
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.5191
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0620.59
X-RAY DIFFRACTIONr_metal_ion_refined0.2240.51
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2810.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.326
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0630.52
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0021.51243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87521969
X-RAY DIFFRACTIONr_scbond_it2.48132013
X-RAY DIFFRACTIONr_scangle_it3.5854.52636
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 82
Rwork0.26 1605
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)
12.80871.0799-2.91962.2748-1.68215.57210.15470.06880.190.509-0.2417-0.0109-0.6450.04340.08690.3294-0.0975-0.11320.05690.03830.1899.2373.51949.397
21.5328-0.08850.59642.7038-1.0362.5977-0.08270.0909-0.00960.2496-0.1785-0.5632-0.090.21710.26120.0643-0.0640.0240.08640.04390.209513.01712.8524.936
33.9934-1.41933.78753.1282-2.44037.9750.2120.4873-0.6712-0.62340.34120.5680.7405-0.7041-0.55330.313-0.233-0.02780.3487-0.05540.169-8.9171.3421.956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1TB1 - 101 - 10
2X-RAY DIFFRACTION1UA18 - 2718 - 27
3X-RAY DIFFRACTION1HC366 - 4261 - 61
4X-RAY DIFFRACTION2TB11 - 1611 - 16
5X-RAY DIFFRACTION2UA12 - 1712 - 17
6X-RAY DIFFRACTION2BE2 - 962 - 96
7X-RAY DIFFRACTION3TB17 - 2717 - 27
8X-RAY DIFFRACTION3UA1 - 111 - 11
9X-RAY DIFFRACTION3AD2 - 972 - 97
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.33
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / Rfactor Rwork: 0.258

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