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- PDB-3bdn: Crystal Structure of the Lambda Repressor -

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Basic information

Entry
Database: PDB / ID: 3bdn
TitleCrystal Structure of the Lambda Repressor
Components
  • DNA (5'-D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DAP*DTP*DAP*DT)-3')
  • DNA (5'-D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DGP*DTP*DAP*DT)-3')
  • Lambda Repressor
KeywordsTRANSCRIPTION/DNA / lambda / repressor / allostery / cooperativity / DNA binding / 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 / core promoter sequence-specific DNA binding / identical protein binding
Similarity search - Function
Umud Fragment, subunit A / Umud Fragment, subunit A / 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 ...Umud Fragment, subunit A / Umud Fragment, subunit A / 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 / Ribbon / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein cI
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.909 Å
AuthorsStayrook, S.E. / Jaru-Ampornpan, P. / Hochschild, A. / Lewis, M.
CitationJournal: Nature / Year: 2008
Title: Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding
Authors: Stayrook, S.E. / Jaru-Ampornpan, P. / Ni, J. / Hochschild, A. / Lewis, M.
History
DepositionNov 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: DNA (5'-D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DAP*DTP*DAP*DT)-3')
D: DNA (5'-D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DGP*DTP*DAP*DT)-3')
A: Lambda Repressor
B: Lambda Repressor


Theoretical massNumber of molelcules
Total (without water)64,3644
Polymers64,3644
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-54.5 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.431, 161.099, 135.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

#1: DNA chain DNA (5'-D(*DAP*DAP*DTP*DAP*DCP*DCP*DAP*DCP*DTP*DGP*DGP*DCP*DGP*DGP*DTP*DGP*DAP*DTP*DAP*DT)-3')


Mass: 6158.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DTP*DAP*DTP*DAP*DTP*DCP*DAP*DCP*DCP*DGP*DCP*DCP*DAP*DGP*DTP*DGP*DGP*DTP*DAP*DT)-3')


Mass: 6108.967 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Lambda Repressor / Repressor protein CI


Mass: 26048.596 Da / Num. of mol.: 2 / Mutation: D197G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Strain: BL21 DE3 / Gene: CI / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P03034

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 14% PEG 4000, 0.1 M Sodium Acetate pH 4.6, 0.2 M Ammonium Sulfate, 0.05 M Magnesium Chloride, 20% Glycerol, 1 mM Spermine, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium Acetate11
3(NH4)2SO411
4MgCl211
5Glycerol11
6spermine11
7PEG 400012
8Sodium Acetate12
9(NH4)2SO412
10MgCl212
11Glycerol12
12spermine12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 15, 2002
RadiationMonochromator: Undulator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.909→34.61 Å / Num. all: 7810 / Num. obs: 7238 / % possible obs: 99 % / Redundancy: 10 % / Biso Wilson estimate: 111 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.2
Reflection shellResolution: 3.909→4.14 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 8 / Num. unique all: 629 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
MLPHAREphasing
REFMAC5.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 1LMB, 1F39

1lmb

1f39


Resolution: 3.909→34.61 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.826 / Rfactor Rfree error: 0.015 / SU B: 95.243 / SU ML: 1.32 / Data cutoff high absF: 5779853.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.163 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.37413 350 4.8 %RANDOM
Rwork0.29211 ---
all0.29597 7238 --
obs0.29597 7238 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT MODEL / Bsol: 115.341 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 170.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.82 Å0.67 Å
Luzzati d res low-5 Å
Luzzati sigma a0.81 Å0.8 Å
Refinement stepCycle: LAST / Resolution: 3.909→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 779 0 0 4405
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0245760.022
X-RAY DIFFRACTIONr_angle_refined_deg1.77363422.194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1834645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.50315825.063
X-RAY DIFFRACTIONr_chiral_restr0.1146910.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00531990.02
X-RAY DIFFRACTIONr_nbd_refined0.30429470.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2592170.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.306450.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.29520.2
X-RAY DIFFRACTIONr_mcbond_it0.70123871.5
X-RAY DIFFRACTIONr_mcangle_it1.13537482
X-RAY DIFFRACTIONr_scbond_it1.16626763
X-RAY DIFFRACTIONr_scangle_it1.52325944.5
LS refinement shellResolution: 3.909→4.01 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.464 23 4.2 %
Rwork0.424 502 -
obs--96.15 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top

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