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- PDB-2ovg: Lambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221 -

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Basic information

Entry
Database: PDB / ID: 2ovg
TitleLambda Cro Q27P/A29S/K32Q triple mutant at 1.35 A in space group P3221
ComponentsPhage lambda Cro
KeywordsTRANSCRIPTION / Transcription factor / helix-turn-helix / bacteriophage / flexibility
Function / homology
Function and homology information


latency-replication decision / release from viral latency / negative regulation of transcription by competitive promoter binding / negative regulation of viral transcription / core promoter sequence-specific DNA binding / response to UV / protein homodimerization activity / DNA binding
Similarity search - Function
CRO Repressor / Regulatory protein cro superfamily / Cro / Regulatory protein cro / CRO Repressor / Lambda repressor-like, DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsHall, B.M. / Heroux, A. / Roberts, S.A. / Cordes, M.H.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Two structures of a lambda Cro variant highlight dimer flexibility but disfavor major dimer distortions upon specific binding of cognate DNA.
Authors: Hall, B.M. / Roberts, S.A. / Heroux, A. / Cordes, M.H.
History
DepositionFeb 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Phage lambda Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6943
Polymers7,3591
Non-polymers3342
Water1,946108
1
A: Phage lambda Cro
hetero molecules

A: Phage lambda Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3886
Polymers14,7192
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Phage lambda Cro
hetero molecules

A: Phage lambda Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3886
Polymers14,7192
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)50.524, 50.524, 48.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsThe asymmetric unit contains a monomer which is half of the biological assembly. The second part of the biological assembly is generated by the two fold axis: -x, y-x, 2/3-z

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Components

#1: Protein Phage lambda Cro


Mass: 7359.418 Da / Num. of mol.: 1 / Mutation: Q27P, A29S, K32Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-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: P03040
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5 M lithium sulfate, 0.1 M Na Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.96 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2005 / Details: mirrors
RadiationMonochromator: Si (111) Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 15657 / Num. obs: 15657 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.067 / Χ2: 1.941 / Net I/σ(I): 14.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.96 / Num. unique all: 1513 / Χ2: 1.719 / % possible all: 96.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.4 Å15.64 Å
Translation1.4 Å15.64 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CRO protein portion

6cro


Resolution: 1.35→43.77 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.494 / SU ML: 0.028 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 788 5 %RANDOM
Rwork0.132 ---
obs0.134 15657 97.77 %-
all-15657 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms454 0 11 108 573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022530
X-RAY DIFFRACTIONr_bond_other_d0.0060.02389
X-RAY DIFFRACTIONr_angle_refined_deg1.291.979723
X-RAY DIFFRACTIONr_angle_other_deg0.8773950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.062571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.04622.69226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4871599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.031156
X-RAY DIFFRACTIONr_chiral_restr0.0960.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02591
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02115
X-RAY DIFFRACTIONr_nbd_refined0.2340.2100
X-RAY DIFFRACTIONr_nbd_other0.1910.2374
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2265
X-RAY DIFFRACTIONr_nbtor_other0.0770.2290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.254
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1350.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.226
X-RAY DIFFRACTIONr_mcbond_it3.0352340
X-RAY DIFFRACTIONr_mcbond_other1.1692124
X-RAY DIFFRACTIONr_mcangle_it3.573512
X-RAY DIFFRACTIONr_scbond_it5.9129236
X-RAY DIFFRACTIONr_scangle_it6.99912203
X-RAY DIFFRACTIONr_rigid_bond_restr2.51131030
X-RAY DIFFRACTIONr_sphericity_free12.2833108
X-RAY DIFFRACTIONr_sphericity_bonded4.8673903
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 61 -
Rwork0.222 1063 -
obs-1124 96.32 %

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