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- PDB-5a7l: TP901-1 CI NTD (res 1-80) -

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Basic information

Entry
Database: PDB / ID: 5a7l
TitleTP901-1 CI NTD (res 1-80)
ComponentsCI
KeywordsTRANSCRIPTION
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
Biological speciesLACTOCOCCUS PHAGE (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.103 Å
AuthorsFrandsen, K.E.H. / Rasmussen, K.K. / Lo Leggio, L.
CitationJournal: Sci.Rep. / Year: 2016
Title: Structural and Dynamics Studies of a Truncated Variant of Ci Repressor from Bacteriophage Tp901-1.
Authors: Rasmussen, K.K. / Frandsen, K.E.H. / Boeri Erba, E. / Pedersen, M. / Varming, A.K. / Hammer, K. / Kilstrup, M. / Thulstrup, P.W. / Blackledge, M. / Jensen, M.R. / Lo Leggio, L.
History
DepositionJul 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: CI


Theoretical massNumber of molelcules
Total (without water)9,1281
Polymers9,1281
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.720, 36.010, 38.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CI / NTD


Mass: 9127.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-80 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS PHAGE (virus) / Strain: TP901-1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O48503
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.39 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 4277 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Redundancy: 3.52 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.68
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 1.73 / % possible all: 87.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZHI

3zhi


Resolution: 2.103→29.911 Å / SU ML: 0.26 / σ(F): 1.37 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 425 10 %
Rwork0.2158 --
obs0.2179 4262 90.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.103→29.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms638 0 0 39 677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004647
X-RAY DIFFRACTIONf_angle_d0.681871
X-RAY DIFFRACTIONf_dihedral_angle_d14.776250
X-RAY DIFFRACTIONf_chiral_restr0.027102
X-RAY DIFFRACTIONf_plane_restr0.003109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1028-2.4070.2941380.26641272X-RAY DIFFRACTION92
2.407-3.03210.28461500.24731260X-RAY DIFFRACTION92
3.0321-29.91450.19951370.19011305X-RAY DIFFRACTION88

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