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

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Basic information

Entry
Database: PDB / ID: 3jxd
TitleCrystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+
Components
  • 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*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
RUBIDIUM ION / DNA / DNA (> 10) / Repressor protein C2
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'
B: 5'-D(*CP*AP*TP*TP*TP*AP*AP*GP*AP*CP*GP*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)27,4246
Polymers27,2534
Non-polymers1712
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-40.9 kcal/mol
Surface area12140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.007, 64.007, 101.623
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*CP*GP*TP*CP*TP*TP*AP*AP*AP*TP*G)-3'


Mass: 6132.003 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic DNA Operator 9C
#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-RB / RUBIDIUM ION / Rubidium


Mass: 85.468 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Rb
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 67.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Rubidium chloride, PEG 400, Tris-HCl, MgCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1Rubidium chloride11
2PEG 40011
3Tris-HClTris11
4MgCl211
5Rubidium chloride12
6PEG 40012
7Tris-HClTris12
8MgCl212

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.34 Å / Num. all: 23743 / Num. obs: 23743 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 12.5 % / Rsym value: 0.142 / Net I/σ(I): 33.2
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 1762 / Rsym value: 0.636 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R1J

2r1j


Resolution: 2.1→41.34 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.557 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.151 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1214 5.1 %RANDOM
Rwork0.18 ---
obs0.183 22529 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 109.79 Å2 / Biso mean: 26.546 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1030 814 2 288 2134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211950
X-RAY DIFFRACTIONr_angle_refined_deg2.2292.5032792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4765130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28923.63644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4381512
X-RAY DIFFRACTIONr_chiral_restr0.1290.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021172
X-RAY DIFFRACTIONr_nbd_refined0.1910.2842
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.2283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.223
X-RAY DIFFRACTIONr_mcbond_it1.1441.5661
X-RAY DIFFRACTIONr_mcangle_it1.95621040
X-RAY DIFFRACTIONr_scbond_it2.90931687
X-RAY DIFFRACTIONr_scangle_it4.2474.51752
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 88 -
Rwork0.241 1674 -
all-1762 -
obs--99.55 %

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