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- PDB-1rzs: Solution structure of P22 Cro -

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Basic information

Entry
Database: PDB / ID: 1rzs
TitleSolution structure of P22 Cro
ComponentsRegulatory protein cro
KeywordsTRANSCRIPTION / HELIX-TURN-HELIX / DNA-BINDING PROTEIN / STRUCTURAL EVOLUTION
Function / homologyDNA-binding transcriptional regulator Cro / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / Regulatory protein cro
Function and homology information
Biological speciesEnterobacteria phage P22 (virus)
MethodSOLUTION NMR / simulated annealing
AuthorsNewlove, T. / Konieczka, J.H. / Cordes, M.H.
CitationJournal: STRUCTURE / Year: 2004
Title: Secondary structure switching in Cro protein evolution.
Authors: Newlove, T. / Konieczka, J.H. / Cordes, M.H.
History
DepositionDec 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein cro


Theoretical massNumber of molelcules
Total (without water)6,8381
Polymers6,8381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 30agreement with distance and angle restraints; two structures were also eliminated due to high energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Regulatory protein cro / Antirepressor


Mass: 6837.767 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Genus: P22-like viruses / Gene: CRO / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P09964

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
122HNHA
132HNHB
1423D 15N-separated NOESY
1533D 13C-separated NOESY
164hydrogen exchange

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Sample preparation

Details
Solution-IDContentsSolvent system
16 mM P22 Cro, 50 mM sodium phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
23.5 mM P22 Cro U-15N, 50 mM sodium phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
32.75 mM P22 Cro U-15N, 13C, 50 mM sodium phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
43.5 mM P22 Cro U-15N, 50 mM sodium phosphate buffer, 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM sodium phosphate 6.4ambient 293 K
250 mM sodium phosphate 6.4ambient 300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukercollection
NMRPipeF. Delaglio et alprocessing
NMRView4.1.3B. Johnsondata analysis
CNS1.1A. Brunger et alstructure solution
CNS1.1A. Brunger et alrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 30 structures were calculated using 916 NOE-derived distance restraints, 10 hydrogen bond distance restraints, 41 phi angle restraints and 5 chi1 angle restraints. 23 of 30 calculated ...Details: 30 structures were calculated using 916 NOE-derived distance restraints, 10 hydrogen bond distance restraints, 41 phi angle restraints and 5 chi1 angle restraints. 23 of 30 calculated structures were initially accepted based on no distance restraint violations greater than 0.4 angstroms and no angle restraint violations greater than 5 degrees. Of the 23, 2 were eliminated for having significantly higher energy than the others, leaving 21 structures in the final ensemble. The ordered region of the structure includes residues 1-57. Pairwise RMSDs for the ordered region were 0.53 A (backbone atoms) and 1.29 A (all heavy atoms). None of the backbone angles in the ordered region of any ensemble member fell outside the most favorable and additionally allowed regions of a Ramachandran plot.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: agreement with distance and angle restraints; two structures were also eliminated due to high energy
Conformers calculated total number: 30 / Conformers submitted total number: 21

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