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- PDB-5hnh: Crystal structure of pyrene- and phenanthrene-modified DNA in com... -

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Basic information

Entry
Database: PDB / ID: 5hnh
TitleCrystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
Components
  • DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*T*(YPY)*(YPY)*C)-3')
  • Restriction endonuclease R.BpuJI
KeywordsHYDROLASE / Phenanthrene / Pyrene / DNA / Endonuclease
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Arc Repressor Mutant, subunit A - #2080 / Arc Repressor Mutant, subunit A - #2090 / Rna Polymerase Sigma Factor; Chain: A - #180 / Restriction endonuclease, type II, BpuJI, N-terminal / Protein NO VEIN, C-terminal / Restriction endonuclease BpuJI - N terminal / Protein NO VEIN, C-terminal / Rna Polymerase Sigma Factor; Chain: A / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Restriction endonuclease R.BpuJI
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.876 Å
AuthorsProbst, M. / Aeschimann, W. / Chau, T.-T.-H. / Langenegger, S.M. / Stocker, A. / Haener, R.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural insight into DNA-assembled oligochromophores: crystallographic analysis of pyrene- and phenanthrene-modified DNA in complex with BpuJI endonuclease.
Authors: Probst, M. / Aeschimann, W. / Chau, T.T. / Langenegger, S.M. / Stocker, A. / Haner, R.
History
DepositionJan 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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: Restriction endonuclease R.BpuJI
L: DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
M: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*T*(YPY)*(YPY)*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,0583
Polymers41,0583
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-17 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.666, 164.402, 44.033
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Restriction endonuclease R.BpuJI


Mass: 33766.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: bpuJIR / Production host: Escherichia coli (E. coli) / References: UniProt: A3FMN7
#2: DNA chain DNA (5'-D(*GP*(YPY)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')


Mass: 3470.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*T*(YPY)*(YPY)*C)-3')


Mass: 3821.705 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Tacsimate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.876→48.287 Å / Num. obs: 35505 / % possible obs: 97.3 % / Redundancy: 3.26 % / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.14
Reflection shellResolution: 1.88→1.99 Å / Redundancy: 3.17 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.93 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLA

2vla


Resolution: 1.876→48.287 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 21.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 3200 4.99 %
Rwork0.1691 --
obs0.1707 35452 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.876→48.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 483 0 171 2927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092880
X-RAY DIFFRACTIONf_angle_d1.0283969
X-RAY DIFFRACTIONf_dihedral_angle_d18.5211096
X-RAY DIFFRACTIONf_chiral_restr0.044416
X-RAY DIFFRACTIONf_plane_restr0.005439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8765-1.90450.3798780.3361520X-RAY DIFFRACTION53
1.9045-1.93420.36031460.31572713X-RAY DIFFRACTION96
1.9342-1.96590.32041360.29832687X-RAY DIFFRACTION97
1.9659-1.99980.30321420.27362831X-RAY DIFFRACTION97
1.9998-2.03620.26681450.23522711X-RAY DIFFRACTION97
2.0362-2.07540.24221420.23122730X-RAY DIFFRACTION96
2.0754-2.11770.25881440.21922745X-RAY DIFFRACTION96
2.1177-2.16380.20111460.19952689X-RAY DIFFRACTION96
2.1638-2.21410.22251500.19312766X-RAY DIFFRACTION97
2.2141-2.26950.24711440.18082675X-RAY DIFFRACTION96
2.2695-2.33080.21671410.17972756X-RAY DIFFRACTION96
2.3308-2.39940.24521400.1822663X-RAY DIFFRACTION95
2.3994-2.47690.2361360.17512687X-RAY DIFFRACTION94
2.4769-2.56540.18731330.17892577X-RAY DIFFRACTION92
2.5654-2.66810.21381360.18122583X-RAY DIFFRACTION92
2.6681-2.78950.23951440.18742700X-RAY DIFFRACTION96
2.7895-2.93660.2651470.18962785X-RAY DIFFRACTION98
2.9366-3.12050.19631490.18232783X-RAY DIFFRACTION98
3.1205-3.36140.20821470.16292727X-RAY DIFFRACTION97
3.3614-3.69960.18381380.14982758X-RAY DIFFRACTION97
3.6996-4.23460.14521420.1352640X-RAY DIFFRACTION95
4.2346-5.33410.15291320.12372481X-RAY DIFFRACTION88
5.3341-48.30260.14911420.13892719X-RAY DIFFRACTION96
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)
12.1597-1.23210.34863.4322-0.45873.24220.16340.3145-0.2632-0.5332-0.1803-0.04520.72260.05680.03290.39240.02180.02330.24810.03570.2872-0.422119.2423-29.0619
21.6647-0.9638-0.40413.641-0.09472.927-0.0798-0.0477-0.03760.28980.16330.2288-0.1202-0.5153-0.08390.23920.03870.01750.3720.07870.2425-11.785832.3476-16.2189
31.9486-0.8791-0.31883.0169-0.93810.4857-0.1218-0.10570.2470.41850.1425-0.1365-0.3744-0.2243-0.02180.37850.07580.0020.3010.01930.2663-6.082539.2094-15.4766
43.25770.5301-0.47945.87621.07133.1303-0.01030.0983-0.55090.08710.13020.53720.5867-0.8077-0.13040.3396-0.1676-0.06390.55670.10520.4639-18.086117.2751-21.7202
54.1676-0.51950.73870.0869-0.31922.20910.0035-0.2469-0.6681-0.0892-0.0014-0.38740.28970.0525-0.05420.442-0.0019-0.00050.26360.08670.42127.72516.9498-15.0452
63.48480.1167-1.14776.5339-0.04217.01090.1124-0.3833-0.3666-0.1027-0.13260.43180.7586-0.26550.1090.2862-0.0398-0.07280.34930.09280.44485.791216.3746-15.0344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 176 )
3X-RAY DIFFRACTION3chain 'A' and (resid 177 through 246 )
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 280 )
5X-RAY DIFFRACTION5chain 'L' and (resid 101 through 111 )
6X-RAY DIFFRACTION6chain 'M' and (resid 201 through 212 )

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