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- PDB-3jxc: Crystal structure of the P22 c2 repressor protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 3jxc
TitleCrystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+
Components
  • 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'
  • Repressor protein C2
KeywordsTRANSCRIPTION REGULATOR / protein-DNA complex / DNA-binding / Repressor / Transcription / Transcription regulation
Function / homology
Function and homology information


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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal 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 / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
THALLIUM (I) ION / DNA / DNA (> 10) / Repressor protein C2
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWatkins, D. / Koudelka, G.B. / Williams, L.D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Sequence Recognition of DNA by Protein-Induced Conformational Transitions.
Authors: Watkins, D. / Mohan, S. / Koudelka, G.B. / Williams, L.D.
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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
A: 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'
B: 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*TP*AP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'
L: Repressor protein C2
R: Repressor protein C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0698
Polymers27,2514
Non-polymers8184
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-41.2 kcal/mol
Surface area12190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.249, 64.249, 100.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
DetailsBiological unit is the same as asymmetric unit.

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Components

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


Mass: 6131.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA Operator 9T
#2: Protein Repressor protein C2 /


Mass: 7494.681 Da / Num. of mol.: 2 / Fragment: N-terminal domain: UNP residues 2-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: C2 / Plasmid: pUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P69202
#3: Chemical
ChemComp-TL / THALLIUM (I) ION / Thallium


Mass: 204.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Tl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O

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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: 3.82 Å3/Da / Density % sol: 67.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 400, Thallium acetate, Tris-HCl, Magnesium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2Thallium acetate11
3Tris-HClTris11
4Magnesium acetate11
5PEG 40012
6Thallium acetate12
7Tris-HClTris12
8Magnesium acetate12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97784 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97784 Å / Relative weight: 1
ReflectionResolution: 1.9→30.61 Å / Num. all: 31737 / Num. obs: 31737 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rsym value: 0.073 / Net I/σ(I): 44.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 9.29 / Num. unique all: 1591 / Rsym value: 0.487 / % possible all: 97.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R1J

2r1j


Resolution: 1.9→30.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 2.428 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1591 5 %RANDOM
Rwork0.184 ---
obs0.185 30146 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.88 Å2 / Biso mean: 25.067 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 814 4 279 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211950
X-RAY DIFFRACTIONr_angle_refined_deg1.6812.5032792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0855130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49423.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30715216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.0361512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021172
X-RAY DIFFRACTIONr_nbd_refined0.1910.2777
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.227
X-RAY DIFFRACTIONr_mcbond_it0.9321.5679
X-RAY DIFFRACTIONr_mcangle_it1.46821040
X-RAY DIFFRACTIONr_scbond_it2.12231708
X-RAY DIFFRACTIONr_scangle_it3.224.51752
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 115 -
Rwork0.24 2199 -
all-2314 -
obs--97.68 %

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