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- PDB-2p5l: Crystal structure of a dimer of N-terminal domains of AhrC in com... -

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Basic information

Entry
Database: PDB / ID: 2p5l
TitleCrystal structure of a dimer of N-terminal domains of AhrC in complex with an 18bp DNA operator site
Components
  • Arginine repressor
  • DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')
  • DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')
Keywordstranscription repressor / DNA-binding domain / winged helix-turn-helix / ARG box / protein-DNA complex
Function / homology
Function and homology information


arginine catabolic process to ornithine / arginine biosynthetic process / arginine binding / protein complex oligomerization / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Arginine repressor / Arginine repressor, C-terminal / Arginine repressor, DNA-binding domain / Arginine repressor, C-terminal domain superfamily / Arginine repressor, DNA binding domain / Arginine repressor, C-terminal domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Arginine repressor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsGarnett, J.A. / Marincs, F. / Baumberg, S. / Stockley, P.G. / Phillips, S.E.V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure and function of the arginine repressor-operator complex from Bacillus subtilis.
Authors: Garnett, J.A. / Marincs, F. / Baumberg, S. / Stockley, P.G. / Phillips, S.E.
History
DepositionMar 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')
B: DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')
E: DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')
F: DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')
C: Arginine repressor
D: Arginine repressor
G: Arginine repressor
H: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,25713
Polymers51,7768
Non-polymers4805
Water23413
1
A: DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')
B: DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')
C: Arginine repressor
D: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9845
Polymers25,8884
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-46 kcal/mol
Surface area10980 Å2
MethodPISA
2
E: DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')
F: DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')
G: Arginine repressor
H: Arginine repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2728
Polymers25,8884
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-75.4 kcal/mol
Surface area11570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.105, 118.770, 121.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Details1 of the 2 complexes (chains A,B,C,D or E,F,G,H) is the biological protein-DNA complex

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Components

#1: DNA chain DNA (5'-D(*DCP*DAP*DTP*DGP*DAP*DAP*DTP*DAP*DAP*DAP*DAP*DAP*DTP*DTP*DCP*DAP*DAP*DG)-3')


Mass: 5540.657 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by MWG-biotech
#2: DNA chain DNA (5'-D(*DCP*DTP*DTP*DGP*DAP*DAP*DTP*DTP*DTP*DTP*DTP*DAP*DTP*DTP*DCP*DAP*DTP*DG)-3')


Mass: 5486.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by MWG-biotech
#3: Protein
Arginine repressor / Arginine hydroxamate resistance protein


Mass: 7430.474 Da / Num. of mol.: 4 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: argR, ahrC / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17893
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.77 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 277 K / pH: 7.1
Details: 1.7M ammonium sulphate, 0.1M HEPES, 0.1M sodium chloride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.10
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium sulphate11
2HEPES11
3sodium chloride11
4H2O11
5ammonium sulphate12
6HEPES12
7sodium chloride12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.85→24.81 Å / Num. obs: 23191 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 18
Reflection shellResolution: 2.85→3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.406 / % possible all: 98

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-TERMINAL DOMAIN OF AHRC (2P5K) AND 7BP OF DNA FROM THE PURINE REPRESSOR-OPERATOR COMPLEX (1JFS)

2p5k

1jfs


Resolution: 2.85→24.81 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.811 / SU ML: 0.204 / TLS residual ADP flag: LIKELY RESIDUAL
Isotropic thermal model: Individual isotropic temperature factors and individual TLS parameters for chains A-H
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.409 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1198 5.2 %RANDOM
Rwork0.207 ---
obs0.208 23191 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.89 Å20 Å20 Å2
2--0.53 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.85→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 1448 25 13 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213804
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6752.465326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2635250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.99825.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63715434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3811512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022255
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.31846
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3460.52397
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.332
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.511
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.69521285
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17332064
X-RAY DIFFRACTIONr_scbond_it0.58723282
X-RAY DIFFRACTIONr_scangle_it0.87433262
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.92 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 76 -
Rwork0.39 1601 -
obs--97.56 %
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)
18.0142.61943.24255.5661.06845.12550.4735-0.1813-1.17470.3989-0.1567-0.60720.7554-0.0122-0.31680.1208-0.0052-0.19-0.0759-0.01990.28335.3745.998-2.736
29.5644.13111.74836.6010.62082.04890.3669-0.0076-1.24390.42510.0095-1.12630.65290.1201-0.37640.1884-0.0336-0.2327-0.07760.02230.22914.4425.859-1.549
311.26970.53250.96544.1420.35194.85760.27920.65290.01170.0562-0.1662-0.447-0.02010.4921-0.1130.0750.0469-0.02260.04550.02030.1839.23921.699-9.365
46.45513.5890.30856.4098-0.08753.13850.2963-0.1328-0.07150.4881-0.32710.29860.5101-0.420.03080.1685-0.0266-0.01050.1251-0.01440.1305-12.08311.852-3.953
52.29560.22862.27371.07080.43847.39230.3662-0.2427-0.07130.2266-0.51010.49790.3057-1.14260.1440.2468-0.2416-0.01420.6032-0.20470.4183-34.558-17.771-30.214
65.2810.8234.0871.08251.72817.58210.4416-0.9223-0.15080.4465-0.51160.23890.7496-1.55510.07010.35-0.33040.00230.6417-0.10880.3709-34.592-19.948-30.24
77.01232.7793-0.10817.5122-0.47167.83890.30590.37950.1803-0.226-0.00690.84610.1296-1.1457-0.2990.01420.021-0.09860.3545-0.05640.1361-36.567-13.175-47.856
85.8767-0.2872-0.99566.13771.93449.64110.0233-0.1193-0.32640.4667-0.0362-0.15240.68560.36960.01290.1002-0.03120.00160.1002-0.0120.0931-15.869-19.41-34.157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 181 - 18
2X-RAY DIFFRACTION2BB1 - 181 - 18
3X-RAY DIFFRACTION3CE2 - 642 - 64
4X-RAY DIFFRACTION4DF1 - 641 - 64
5X-RAY DIFFRACTION5EC1 - 181 - 18
6X-RAY DIFFRACTION6FD2 - 182 - 18
7X-RAY DIFFRACTION7GG2 - 642 - 64
8X-RAY DIFFRACTION8HH1 - 641 - 64

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