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- PDB-2ecs: Lambda Cro mutant Q27P/A29S/K32Q at 1.4 A in space group C2 -

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Basic information

Entry
Database: PDB / ID: 2ecs
TitleLambda Cro mutant Q27P/A29S/K32Q at 1.4 A in space group C2
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 viral transcription / negative regulation of transcription by competitive promoter binding / 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
ACETATE ION / : / Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHall, B.M. / 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 14, 2007Deposition site: PDBJ / 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 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 1.3Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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
B: Phage lambda Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,38913
Polymers14,7192
Non-polymers67011
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-62 kcal/mol
Surface area8370 Å2
MethodPISA, PQS
2
B: Phage lambda Cro
hetero molecules

B: Phage lambda Cro
hetero molecules

A: Phage lambda Cro
hetero molecules

A: Phage lambda Cro
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,77726
Polymers29,4384
Non-polymers1,34022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area7840 Å2
ΔGint-159 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.689, 26.999, 55.523
Angle α, β, γ (deg.)90.00, 103.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phage lambda Cro


Mass: 7359.418 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 172 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 80% saturated lithium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.4→53.946 Å / Num. all: 25562 / Num. obs: 25562 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 5.8
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 1.7 / Num. measured all: 19965 / Num. unique all: 3680 / % possible all: 100

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å25.74 Å
Translation2.5 Å25.74 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Lambda Cro Q27P/A29S/K32Q at 1.35 A resolution in space group P3221

Resolution: 1.4→53.92 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.831 / SU ML: 0.033 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1300 5.1 %RANDOM
Rwork0.139 ---
obs0.141 25561 99.82 %-
all-25561 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.014 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å2-0.4 Å2
2---0.92 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.4→53.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms942 0 39 161 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221017
X-RAY DIFFRACTIONr_bond_other_d0.0010.02691
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9931367
X-RAY DIFFRACTIONr_angle_other_deg0.95131690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.0735123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.20923.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57815183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.655156
X-RAY DIFFRACTIONr_chiral_restr0.1020.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021097
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined0.2290.2197
X-RAY DIFFRACTIONr_nbd_other0.1940.2624
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2482
X-RAY DIFFRACTIONr_nbtor_other0.0840.2513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.290
X-RAY DIFFRACTIONr_metal_ion_refined0.3330.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.228
X-RAY DIFFRACTIONr_mcbond_it3.8622823
X-RAY DIFFRACTIONr_mcbond_other2.0722245
X-RAY DIFFRACTIONr_mcangle_it4.3623995
X-RAY DIFFRACTIONr_scbond_it7.2819453
X-RAY DIFFRACTIONr_scangle_it8.75312370
X-RAY DIFFRACTIONr_rigid_bond_restr3.63432092
X-RAY DIFFRACTIONr_sphericity_free15.1153164
X-RAY DIFFRACTIONr_sphericity_bonded8.9731696
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 119 -
Rwork0.196 1758 -
obs-1877 100 %

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