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- PDB-6on0: STRUCTURE OF N15 CRO COMPLEXED WITH CONSENSUS OPERATOR DNA -

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Basic information

Entry
Database: PDB / ID: 6on0
TitleSTRUCTURE OF N15 CRO COMPLEXED WITH CONSENSUS OPERATOR DNA
Components
  • DNA (5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)-3')
  • Gp39CD154
Keywordstranscription/dna / TRANSCRIPTION REPRESSOR-DNA complex / Helix-turn-helix / lambda repressor-like DNA-binding domain / structural evolution / transcription-dna complex
Function / homology
Function and homology information


DNA-binding transcriptional regulator Cro / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Repressor protein
Similarity search - Component
Biological speciesEscherichia phage N15 (virus)
Enterobacteria phage N15 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHall, B.M. / Roberts, S.A. / Cordes, M.H.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-0643790 United States
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the lambda Cro complex.
Authors: Hall, B.M. / Roberts, S.A. / Cordes, M.H.J.
History
DepositionApr 19, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMay 15, 2019ID: 3QWS
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 22, 2021Group: Data collection / Database references / Category: database_2 / reflns_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.5Oct 11, 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: Gp39
B: Gp39
C: DNA (5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)-3')
N: DNA (5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)26,0814
Polymers26,0814
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-35 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.640, 56.640, 195.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Gp39 / CD154 / Repressor protein


Mass: 7839.874 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage N15 (virus) / Gene: cro, gene 39 / Plasmid: pMD104 (pET21b-derived) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q37964
#2: DNA chain DNA (5'-D(*TP*TP*TP*AP*TP*AP*GP*CP*TP*AP*GP*CP*TP*AP*TP*AP*A)-3')


Mass: 5200.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage N15 (virus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.4 M ammonium phosphate monobasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.6→28.7 Å / Num. obs: 42733 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Net I/σ(I): 13.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.8 / Mean I/σ(I) obs: 6.7 / Num. unique obs: 1762 / CC1/2: 0.214 / Rpim(I) all: 1.7 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HIN

2hin


Resolution: 1.6→28.31 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.906 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.116 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21724 1267 5 %RANDOM
Rwork0.20581 ---
obs0.20639 24273 59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.492 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.05 Å2
Refinement stepCycle: 1 / Resolution: 1.6→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 673 0 144 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121785
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181365
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.4442555
X-RAY DIFFRACTIONr_angle_other_deg1.5491.9853197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5145130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.34721.85254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.00815187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.541158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021541
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02356
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4520.683515
X-RAY DIFFRACTIONr_mcbond_other0.4450.681514
X-RAY DIFFRACTIONr_mcangle_it0.7951.025645
X-RAY DIFFRACTIONr_mcangle_other0.7951.026646
X-RAY DIFFRACTIONr_scbond_it0.8070.9611270
X-RAY DIFFRACTIONr_scbond_other0.8070.9561268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3421.4271907
X-RAY DIFFRACTIONr_long_range_B_refined5.0119.5312279
X-RAY DIFFRACTIONr_long_range_B_other4.9689.1072251
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 7 -
Rwork0.286 190 -
obs--6.29 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.68120.2545-0.92856.7371-1.62612.0368-0.1071-0.12160.2110.3395-0.08180.4599-0.0453-0.61020.18880.23530.01140.03750.0406-0.02150.1001-14.60324.928.527
22.8778-0.07190.28412.71740.84065.4792-0.1196-0.11060.05410.2361-0.0259-0.0214-0.02060.03870.14550.26260.0335-0.02410.06150.03630.0759-6.59527.25227.011
34.61773.41360.25877.78231.20094.7074-0.02130.10740.0353-0.0648-0.08640.1419-0.0036-0.19690.10780.19040.016-0.01120.09110.02380.0847-13.06620.95518.177
429.6288-4.3905-0.86310.13644.08534.98980.07640.4469-0.1518-0.6224-0.43911.1401-0.5571-0.59560.36280.21760.0592-0.16860.20130.01650.312-22.47223.77112.002
57.6257-2.18442.92818.3377-4.90216.5142-0.13260.645-0.3462-0.69970.0233-0.05541.698-0.33750.10940.3618-0.12970.05090.111-0.05940.0362-8.16411.241-0.426
66.58091.4333-1.42374.9581-1.48746.9101-0.30040.71210.0479-0.56140.0509-0.0329-0.0548-0.37770.24950.3565-0.0483-0.01270.22590.02790.0179-5.36620.53-2.989
77.44140.433-2.51383.4893-0.42676.6792-0.23710.1462-0.1089-0.3085-0.0005-0.13510.14170.08410.23760.2755-0.041400.08450.03630.0837-6.11216.7117.282
80.81582.64560.162912.2528-3.9216.28450.04980.0479-0.1279-0.36440.068-0.12090.58810.0574-0.11780.2973-0.05260.00760.0913-0.03070.162-12.2578.26612.373
90.6829-0.389-0.39450.98391.89238.3292-0.08980.07630.1013-0.19040.1314-0.2052-0.54380.935-0.04160.2722-0.10710.00780.23940.08060.09955.65128.39511.012
100.7566-0.3726-0.73232.02391.55865.3532-0.06210.02030.1594-0.23470.1689-0.2083-0.46380.6012-0.10680.2802-0.1099-0.05310.18690.06380.08033.84331.25315.123
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 14
2X-RAY DIFFRACTION2A15 - 34
3X-RAY DIFFRACTION3A35 - 53
4X-RAY DIFFRACTION4A54 - 62
5X-RAY DIFFRACTION5B1 - 10
6X-RAY DIFFRACTION6B11 - 30
7X-RAY DIFFRACTION7B31 - 48
8X-RAY DIFFRACTION8B49 - 63
9X-RAY DIFFRACTION9C1 - 17
10X-RAY DIFFRACTION10N1 - 17

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