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

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Basic information

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


Helix-turn-helix domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / 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
IODIDE ION / DNA / DNA (> 10) / Csp231I C protein
Similarity search - Component
Biological speciesCitrobacter sp. RFL231 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 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 ...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: Csp231I C protein
B: Csp231I C protein
C: DNA (5'-D(*AP*AP*AP*CP*TP*AP*AP*GP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*CP*AP*A)-3')
D: DNA (5'-D(*TP*TP*GP*CP*TP*AP*AP*GP*AP*TP*TP*TP*TP*CP*TP*TP*AP*GP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1498
Polymers35,6414
Non-polymers5084
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-53 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.340, 62.340, 158.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IS A PROTEIN DIMER BOUND TO DNA DUPLEX.

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Components

#1: Protein Csp231I C protein


Mass: 11380.236 Da / Num. of mol.: 2
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*AP*AP*CP*TP*AP*AP*GP*AP*AP*AP*AP*TP*CP*TP*TP*AP*GP*CP*AP*A)-3')


Mass: 6456.252 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*GP*CP*TP*AP*AP*GP*AP*TP*TP*TP*TP*CP*TP*TP*AP*GP*TP*TP*T)-3')


Mass: 6424.164 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) ...Details: Protein was dialysed against the buffer containing 0.1 M NaCl, 50 mM TRIS-HCl pH 8.0, 1 mM EDTA. Crystallisation conditions: 0.2 M sodium iodide, 0.1 M Bis-Tris Propane pH 6.0, 15 % (w/v) PEG3350, 10 mM spermidine, protein dimer/DNA molar ratio 1:1, protein concentration 4.6 mg/ml , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.971
11K, H, -L20.029
ReflectionResolution: 1.8→53.99 Å / Num. all: 32091 / Num. obs: 30476 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.6 / % possible all: 99.8

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Processing

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

3lfp


Resolution: 1.8→53.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.104 / SU ML: 0.033 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1626 1614 5 %RANDOM
Rwork0.14712 ---
obs0.14788 30476 99.9 %-
all-32091 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 855 4 402 2755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0162474
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9521.6453511
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0415182
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.75123.68476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32915296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6641516
X-RAY DIFFRACTIONr_chiral_restr0.0660.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021573
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 109 -
Rwork0.157 2270 -
obs--99.83 %
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)
12.4308-0.81580.31852.4567-0.35120.75720.07070.21350.1554-0.073-0.089-0.3716-0.11020.1340.01830.0674-0.0320.01860.07660.01910.069157.610340.8242-9.7151
21.4186-0.07420.22222.9054-0.64621.56910.0289-0.03840.13570.219-0.0688-0.2845-0.1970.17330.03990.0514-0.016-0.02010.0527-0.00320.068564.103629.51384.1947
30.998-0.60770.37773.1956-1.36310.87110.0942-0.0056-0.246-0.010.04120.44630.0847-0.0423-0.13540.0874-0.04770.00140.1178-0.01680.115342.37324.4942-2.7016
41.8472-1.23911.01092.0975-1.14160.81150.0207-0.0339-0.2710.00940.14220.3914-0.0014-0.1278-0.1630.0933-0.02750.01160.1211-0.01710.119242.305524.4521-2.8378
50.4464-0.51760.30131.116-0.51360.51080.0028-0.006-0.0154-0.0129-0.00150.03570.0228-0.0355-0.00130.1491-0.02720.01390.1717-0.02030.168952.050428.668-2.4486
63.8207-0.8265-2.22435.34544.40074.2778-0.3629-0.2235-0.2734-0.0408-0.21490.59860.1099-0.05820.57780.13190.06310.00910.0639-0.01420.152356.75232.7727-2.6715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 92
2X-RAY DIFFRACTION2B1 - 92
3X-RAY DIFFRACTION3C1 - 21
4X-RAY DIFFRACTION4D1 - 21
5X-RAY DIFFRACTION5A201 - 310
6X-RAY DIFFRACTION5B201 - 318
7X-RAY DIFFRACTION5C101 - 188
8X-RAY DIFFRACTION5D101 - 186
9X-RAY DIFFRACTION6A101 - 102
10X-RAY DIFFRACTION6B101 - 102

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