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- PDB-3clc: Crystal Structure of the Restriction-Modification Controller Prot... -

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Basic information

Entry
Database: PDB / ID: 3clc
TitleCrystal Structure of the Restriction-Modification Controller Protein C.Esp1396I Tetramer in Complex with its Natural 35 Base-Pair Operator
Components
  • (35-MER) x 2
  • Regulatory protein
KeywordsTRANSCRIPTION REGULATOR/DNA / protein-DNA complex / transcriptional regulator / helix-turn-helix / DNA-bending / TRANSCRIPTION REGULATOR-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / 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
DNA / DNA (> 10) / Regulatory protein
Similarity search - Component
Biological speciesEnterobacter sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsMcGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.B. / Kneale, G.G.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural analysis of the genetic switch that regulates the expression of restriction-modification genes.
Authors: McGeehan, J.E. / Streeter, S.D. / Thresh, S.J. / Ball, N. / Ravelli, R.B. / Kneale, G.G.
History
DepositionMar 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Regulatory protein
B: Regulatory protein
C: Regulatory protein
D: Regulatory protein
E: 35-MER
F: 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6648
Polymers59,6166
Non-polymers492
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-75.9 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.480, 104.480, 139.290
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13E
23F

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLULYSLYSAA2 - 775 - 80
21GLUGLULYSLYSDD2 - 775 - 80
12GLUGLULYSLYSBB2 - 775 - 80
22GLUGLULYSLYSCC2 - 775 - 80
13DADADTDTEE1 - 351 - 35
23DADADTDTFF1 - 351 - 35

NCS ensembles :
ID
1
2
3
DetailsThe biological unit is the same as the asymmetric unit. There are two orientations of the nucleoprotein complex in the crystal related by a 2-fold axis parallel to the crystallographic b-axis

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Components

#1: Protein
Regulatory protein


Mass: 9521.175 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter sp. (bacteria) / Strain: RFL1396 / Gene: esp1396IC / Plasmid: pET23 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q8GGH0
#2: DNA chain 35-MER


Mass: 10791.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised DNA
#3: DNA chain 35-MER


Mass: 10738.960 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesised DNA
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.68 Å3/Da / Density % sol: 66.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, 40 mM MgCl2, 25% MPD, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2MgCl211
3MPD11
4H2O11
5MES12
6MgCl212
7MPD12
8H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9322 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9322 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 21194 / Num. obs: 21198 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 63.204 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 33.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.8-2.90.3934.813072210398.5
2.9-30.2756.911543182399.9
3-40.07422.762794992699.9
4-50.0285622064353399.9
5-60.02860.49658157499.9
6-80.021697590124599.5
8-100.01289.8279645199.8
10-150.01290.3182731994.7
150.013913657149

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å29.63 Å
Translation3.2 Å29.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→19.06 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 28.854 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.567 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1086 5.1 %RANDOM
Rwork0.207 ---
obs0.209 21157 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 1429 2 4 3931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224140
X-RAY DIFFRACTIONr_angle_refined_deg1.3282.4245853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5565307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06524.314102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.80515569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.411516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022471
X-RAY DIFFRACTIONr_nbd_refined0.2950.21997
X-RAY DIFFRACTIONr_nbtor_refined0.3380.22717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2139
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3410.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0340.21
X-RAY DIFFRACTIONr_mcbond_it1.1171.51569
X-RAY DIFFRACTIONr_mcangle_it1.68922488
X-RAY DIFFRACTIONr_scbond_it2.15933355
X-RAY DIFFRACTIONr_scangle_it3.3884.53365
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A631TIGHT POSITIONAL0.10.05
1A631TIGHT THERMAL0.090.5
2B612TIGHT POSITIONAL0.070.05
2B612TIGHT THERMAL0.090.5
3E407TIGHT POSITIONAL0.050.05
3E407TIGHT THERMAL0.170.5
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 80 -
Rwork0.365 1451 -
all-1531 -
obs--100 %
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)
19.9884-1.2002-4.63883.90051.72938.6104-0.4424-0.04390.2709-0.35560.4805-1.0489-0.06520.3086-0.0381-0.77470.13590.0063-0.3736-0.1625-0.601388.2-23.08-17.35
214.15631.5203-3.15166.44670.20446.6921-0.0758-0.46160.08240.4230.51130.74980.2764-0.1314-0.4355-0.82820.1164-0.0025-0.50980.0106-0.732670.11-23.24-6.65
313.3995-1.9818-2.83527.0366-0.41877.6958-0.04330.46480.0481-0.37610.4001-0.78620.21680.1313-0.3568-0.8544-0.11480.0059-0.572-0.0037-0.743634.48-23.17-15.85
48.93791.4168-3.97584.2048-1.57387.83-0.34110.10280.19030.39240.45420.9762-0.1293-0.2138-0.1131-0.7818-0.10210.0095-0.41420.146-0.619516.31-23.12-5.24
519.5205-0.8443-6.73360.91510.50732.8939-0.02260.1818-1.05920.04270.12050.02860.3429-0.1536-0.0979-0.5913-0.0089-0.1301-0.47440.0163-0.617452.28-27.19-10.95
618.69081.1349-6.04651.1808-0.63322.446-0.0076-0.1834-1.1598-0.0440.0673-0.04120.30740.228-0.0597-0.64110.0341-0.1705-0.4333-0.0122-0.649452.24-27.18-11.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 775 - 80
2X-RAY DIFFRACTION2BB2 - 775 - 80
3X-RAY DIFFRACTION3CC2 - 775 - 80
4X-RAY DIFFRACTION4DD2 - 775 - 80
5X-RAY DIFFRACTION5EE1 - 351 - 35
6X-RAY DIFFRACTION6FF1 - 351 - 35

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