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- PDB-4jqd: Crystal structure of the Restriction-Modification Controller Prot... -

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Basic information

Entry
Database: PDB / ID: 4jqd
TitleCrystal structure of the Restriction-Modification Controller Protein C.Csp231I OL operator complex
Components
  • Csp231I C protein
  • DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')
KeywordsTRANSCRIPTION/DNA / helix-turn-helix / C controller protein / restriction-modification systems / transcriptional regulation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Csp231I C protein
Similarity search - Component
Biological speciesCitrobacter sp. RFL231 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsShevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / McGeehan, J.E. / Kneale, G.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural analysis of DNA binding by C.Csp231I, a member of a novel class of R-M controller proteins regulating gene expression.
Authors: Shevtsov, M.B. / Streeter, S.D. / Thresh, S.J. / Swiderska, A. / McGeehan, J.E. / Kneale, G.G.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csp231I C protein
B: Csp231I C protein
C: DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')
E: Csp231I C protein
F: Csp231I C protein
G: DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)71,2848
Polymers71,2848
Non-polymers00
Water91951
1
A: Csp231I C protein
B: Csp231I C protein
G: DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
H: DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)35,6424
Polymers35,6424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-58 kcal/mol
Surface area15990 Å2
MethodPISA
2
C: DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')
D: DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')
E: Csp231I C protein
F: Csp231I C protein


Theoretical massNumber of molelcules
Total (without water)35,6424
Polymers35,6424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-59 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.120, 128.070, 78.540
Angle α, β, γ (deg.)90.00, 99.99, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A PROTEIN DIMER BOUND TO DNA DUPLEX. THE ASYMMETRIC UNIT CONTAINS TWO PROTEIN-DNA COMPLEXES.

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Components

#1: Protein
Csp231I C protein


Mass: 11380.236 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter sp. RFL231 (bacteria) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: Q32WH4
#2: DNA chain DNA (5'-D(*AP*CP*AP*CP*TP*AP*AP*GP*GP*AP*AP*AP*AP*CP*TP*TP*AP*GP*TP*AP*A)-3')


Mass: 6472.251 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*AP*CP*TP*AP*AP*GP*TP*TP*TP*TP*CP*CP*TP*TP*AP*GP*TP*GP*T)-3')


Mass: 6409.153 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.2, 1 mM DTT, and 1 mM EDTA. Crystallisation conditions: 0.2 M sodium nitrate, 0.1 M Bis-Tris-Propane pH 7. ...Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.2, 1 mM DTT, and 1 mM EDTA. Crystallisation conditions: 0.2 M sodium nitrate, 0.1 M Bis-Tris-Propane pH 7.5, 24 % (w/v) PEG3350, protein dimer/DNA molar ratio 1:1, protein concentration 1.46 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.75→36 Å / Num. all: 20836 / Num. obs: 20336 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9
Reflection shellResolution: 2.75→2.94 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3378 / % possible all: 89

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3LFP

3lfp


Resolution: 2.75→35.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 29.628 / SU ML: 0.267 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23532 1041 5.1 %RANDOM
Rwork0.20511 ---
obs0.20672 19280 97.49 %-
all-20833 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.19 Å2
2--0.19 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.75→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 1710 0 51 4837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0165046
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8631.657152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4335376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69923.462156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6915619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9361535
X-RAY DIFFRACTIONr_chiral_restr0.0820.2711
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023213
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 70 -
Rwork0.402 1154 -
obs-1154 78.11 %
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)
15.89070.2478-2.02722.223-0.51163.31340.08090.2509-0.1371-0.1037-0.099-0.05590.1870.21980.01810.13340.0321-0.08580.0486-0.01930.3271-2.3137-34.4433186.9655
25.52-1.3383-1.59075.5151-0.39185.71540.31990.54890.3034-0.3074-0.1138-0.0615-0.32070.0474-0.20610.18380.012-0.02740.06490.04770.3285-2.8001-16.262182.8177
32.6108-0.8026-0.56875.90670.06181.90590.27910.20360.1463-0.3741-0.3893-0.619-0.19920.35880.11020.2097-0.01520.0090.12920.05020.3497-1.5873-31.5634149.4808
46.1593-0.8929-2.28792.08590.14763.2063-0.089-0.233-0.46230.0432-0.06850.03350.2627-0.02530.15750.149-0.0169-0.06330.02090.02920.3525-18.3006-43.3284161.3685
56.30451.2495-1.34746.2241-0.30574.64330.3606-0.45540.41660.3951-0.13890.1945-0.32640.0449-0.22160.1913-0.025-0.03330.0348-0.04340.2788-17.5239-24.7864164.6568
62.37991.416-0.56476.7162-0.5912.07590.3971-0.13130.28090.307-0.4260.6227-0.3371-0.23820.02890.20850.02170.02650.0713-0.05380.3841-18.5154-22.4854198.7889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 94
2X-RAY DIFFRACTION2B1 - 94
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION3D1 - 21
5X-RAY DIFFRACTION4E1 - 94
6X-RAY DIFFRACTION5F1 - 93
7X-RAY DIFFRACTION6G1 - 21
8X-RAY DIFFRACTION6H1 - 21

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