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- PDB-3zhm: N-terminal domain of the CI repressor from bacteriophage TP901-1 ... -

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Basic information

Entry
Database: PDB / ID: 3zhm
TitleN-terminal domain of the CI repressor from bacteriophage TP901-1 in complex with the OL2 operator half-site
Components
  • 5'-D(*AP*CP*GP*TP*GP*AP*AP*CP*TP*TP*GP*CP*AP*CP *TP*TP*GP*A)-3'
  • 5'-D(*AP*GP*TP*TP*CP*AP*CP*GP*TP*TP*CP*AP*AP*GP *TP*GP*CP*A)-3'
  • CI
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


latency-replication decision / DNA binding
Similarity search - Function
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) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / CI
Similarity search - Component
Biological speciesLACTOCOCCUS PHAGE TP901-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFrandsen, K.H. / Rasmussen, K.K. / Poulsen, J.N. / Lo Leggio, L.
CitationJournal: Biochemistry / Year: 2013
Title: Binding of the N-Terminal Domain of the Lactococcal Bacteriophage Tp901-1 Ci Repressor to its Target DNA: A Crystallography, Small Angle Scattering, and Nuclear Magnetic Resonance Study.
Authors: Frandsen, K.H. / Rasmussen, K.K. / Jensen, M.R. / Hammer, K. / Pedersen, M. / Poulsen, J.N. / Arleth, L. / Lo Leggio, L.
History
DepositionDec 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Data collection
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CI
B: 5'-D(*AP*GP*TP*TP*CP*AP*CP*GP*TP*TP*CP*AP*AP*GP *TP*GP*CP*A)-3'
C: 5'-D(*AP*CP*GP*TP*GP*AP*AP*CP*TP*TP*GP*CP*AP*CP *TP*TP*GP*A)-3'


Theoretical massNumber of molelcules
Total (without water)20,1373
Polymers20,1373
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-18.7 kcal/mol
Surface area7180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.860, 64.070, 67.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CI / CI REPRESSOR


Mass: 9105.513 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-74
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS PHAGE TP901-1 (virus) / Plasmid: PQE-70 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: O48503
#2: DNA chain 5'-D(*AP*GP*TP*TP*CP*AP*CP*GP*TP*TP*CP*AP*AP*GP *TP*GP*CP*A)-3' / OL2 OPERATOR HALF-SITE


Mass: 5515.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) LACTOCOCCUS PHAGE TP901-1 (virus)
#3: DNA chain 5'-D(*AP*CP*GP*TP*GP*AP*AP*CP*TP*TP*GP*CP*AP*CP *TP*TP*GP*A)-3' / OL2 OPERATOR HALF-SITE


Mass: 5515.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) LACTOCOCCUS PHAGE TP901-1 (virus)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOLIGONUCLEOTIDES WERE PURCHASED FROM TAG COPENHAGEN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.45 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.6→33.91 Å / Num. obs: 4365 / % possible obs: 100 % / Observed criterion σ(I): 1.36 / Redundancy: 4.4 % / Biso Wilson estimate: 22.41 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R1J

2r1j


Resolution: 2.6→33.91 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 445 10.37 %
Rwork0.1989 --
obs0.2009 4332 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→33.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms639 362 0 56 1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021057
X-RAY DIFFRACTIONf_angle_d0.6711496
X-RAY DIFFRACTIONf_dihedral_angle_d21.816421
X-RAY DIFFRACTIONf_chiral_restr0.039169
X-RAY DIFFRACTIONf_plane_restr0.002127
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6002-2.97630.26581480.25481260X-RAY DIFFRACTION100
2.9763-3.74910.22891450.19921282X-RAY DIFFRACTION100
3.7491-33.91290.18731520.17261345X-RAY DIFFRACTION100

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