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- PDB-2hin: Structure of N15 Cro at 1.05 A: an ortholog of lambda Cro with a ... -

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Basic information

Entry
Database: PDB / ID: 2hin
TitleStructure of N15 Cro at 1.05 A: an ortholog of lambda Cro with a completely different but equally effective dimerization mechanism
ComponentsRepressor protein
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / DIMER INTERFACE / HELIX-TURN-HELIX
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 / Repressor protein
Function and homology information
Biological speciesEnterobacteria phage N15 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ACORN (Ddirect method) / Resolution: 1.05 Å
AuthorsDubrava, M.S. / Ingram, W.M. / Roberts, S.A. / Weichsel, A. / Montfort, W.R. / Cordes, M.H.
CitationJournal: Protein Sci. / Year: 2008
Title: N15 Cro and lambda Cro: orthologous DNA-binding domains with completely different but equally effective homodimer interfaces.
Authors: Dubrava, M.S. / Ingram, W.M. / Roberts, S.A. / Weichsel, A. / Montfort, W.R. / Cordes, M.H.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Repressor protein
B: Repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8724
Polymers15,6802
Non-polymers1922
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.579, 49.512, 43.768
Angle α, β, γ (deg.)90.000, 91.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Repressor protein / Gp39


Mass: 7839.874 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage N15 (virus) / Genus: N15-like viruses / Gene: cro (gene 39) / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q37964
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.76 Å3/Da / Density % sol: 30.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, 1.8 M ammonium sulfate, 17.5 mg/mL protein, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2006
Details: flat collimating mirror double crystal monochromator toroid focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.05→25.57 Å / Num. all: 49888 / Num. obs: 49888 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.19 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.94 / Net I/σ(I): 9.3 / Scaling rejects: 1582
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.05-1.093.630.4062.11757548420.5396.1
1.09-1.133.630.362.51774848870.696.6
1.13-1.183.640.3242.81797849410.6697
1.18-1.243.650.2643.41803849400.797.6
1.24-1.323.660.2024.41833850060.7398.3
1.32-1.433.690.1555.51852550210.7498.6
1.43-1.573.70.1138.21859750240.8799.3
1.57-1.84.360.10710.92229650970.9899.7
1.8-2.267.310.116.53762050891.3399.9
2.26-25.574.590.05124.52414350411.4797

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
d*TREKdata reduction
ACORNphasing
RefinementMethod to determine structure: ACORN (Ddirect method)
Starting model: 10-RESIDUE ALPHA-HELIX

Resolution: 1.05→24.75 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.996 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.173 2512 5 %RANDOM
Rwork0.16 ---
all0.16 49887 --
obs0.16 49887 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.685 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.18 Å2
2---0.05 Å20 Å2
3---0.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.124 Å
Refinement stepCycle: LAST / Resolution: 1.05→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 10 154 1439
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221321
X-RAY DIFFRACTIONr_bond_other_d0.0020.02933
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9681799
X-RAY DIFFRACTIONr_angle_other_deg0.89332281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83924.30865
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45315243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8881511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021549
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02268
X-RAY DIFFRACTIONr_nbd_refined0.2230.2305
X-RAY DIFFRACTIONr_nbd_other0.1790.2891
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2606
X-RAY DIFFRACTIONr_nbtor_other0.0860.2589
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2103
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.227
X-RAY DIFFRACTIONr_mcbond_it1.76121051
X-RAY DIFFRACTIONr_mcbond_other0.7562329
X-RAY DIFFRACTIONr_mcangle_it2.16131317
X-RAY DIFFRACTIONr_scbond_it3.3996588
X-RAY DIFFRACTIONr_scangle_it4.3589482
X-RAY DIFFRACTIONr_rigid_bond_restr1.81532742
X-RAY DIFFRACTIONr_sphericity_free6.2973154
X-RAY DIFFRACTIONr_sphericity_bonded3.03632218
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 188 -
Rwork0.239 3401 -
obs-3401 95.83 %

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