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

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Basic information

Entry
Database: PDB / ID: 5hnf
TitleCrystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
Components
  • DNA (5'-D(*GP*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*(YPF)P*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: 1.546 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*(YPE)P*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
M: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*(YPF)P*C)-3')


Theoretical massNumber of molelcules
Total (without water)40,6343
Polymers40,6343
Non-polymers00
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-20 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.723, 59.278, 44.048
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-419-

HOH

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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*(YPE)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*TP*(YPF)P*C)-3')


Mass: 3397.321 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Ammonium citrate, 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: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.546→43.93 Å / Num. obs: 61076 / % possible obs: 98 % / Redundancy: 3.17 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.7
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 3.12 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 3.03 / % possible all: 95.1

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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: 1.546→43.93 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 19.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1955 5615 5 %
Rwork0.1706 --
obs0.1719 61042 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.546→43.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 460 0 479 3258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112906
X-RAY DIFFRACTIONf_angle_d1.2364000
X-RAY DIFFRACTIONf_dihedral_angle_d18.6121122
X-RAY DIFFRACTIONf_chiral_restr0.058420
X-RAY DIFFRACTIONf_plane_restr0.007448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5464-1.56390.26041430.25112690X-RAY DIFFRACTION68
1.5639-1.58230.29251860.2473465X-RAY DIFFRACTION90
1.5823-1.60160.29841880.25053549X-RAY DIFFRACTION91
1.6016-1.62190.2861810.23273478X-RAY DIFFRACTION91
1.6219-1.64330.22991830.22943575X-RAY DIFFRACTION92
1.6433-1.66580.27491810.22063496X-RAY DIFFRACTION91
1.6658-1.68960.2421940.21323604X-RAY DIFFRACTION91
1.6896-1.71480.23681810.21373538X-RAY DIFFRACTION92
1.7148-1.74160.251850.21083537X-RAY DIFFRACTION91
1.7416-1.77010.22151890.20323546X-RAY DIFFRACTION92
1.7701-1.80070.20781800.19433473X-RAY DIFFRACTION90
1.8007-1.83340.19621780.18653501X-RAY DIFFRACTION90
1.8334-1.86870.20581860.18553457X-RAY DIFFRACTION90
1.8687-1.90680.21721810.1823483X-RAY DIFFRACTION89
1.9068-1.94830.22091840.18143410X-RAY DIFFRACTION90
1.9483-1.99360.17912030.16953732X-RAY DIFFRACTION95
1.9936-2.04350.20271900.16193645X-RAY DIFFRACTION95
2.0435-2.09870.17911940.16463691X-RAY DIFFRACTION95
2.0987-2.16050.18791900.16073665X-RAY DIFFRACTION96
2.1605-2.23020.19761930.16993709X-RAY DIFFRACTION96
2.2302-2.30990.2221960.16683717X-RAY DIFFRACTION95
2.3099-2.40240.22021960.16883613X-RAY DIFFRACTION95
2.4024-2.51170.19551950.17153651X-RAY DIFFRACTION94
2.5117-2.64410.19991970.1693755X-RAY DIFFRACTION96
2.6441-2.80970.2091950.16723686X-RAY DIFFRACTION96
2.8097-3.02660.20421860.16743579X-RAY DIFFRACTION93
3.0266-3.33110.1871740.15043356X-RAY DIFFRACTION86
3.3311-3.81290.1671860.14513554X-RAY DIFFRACTION92
3.8129-4.80290.14171940.14993819X-RAY DIFFRACTION98
4.8029-43.94760.17222060.16333784X-RAY DIFFRACTION98
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)
11.1377-0.2396-0.03320.80220.04690.7874-0.0518-0.1923-0.06460.07480.0346-0.0820.00830.1457-0.0020.08920.0125-0.00120.13050.01020.1056-20.6311-31.727830.9002
20.6301-0.4904-0.00910.4490.07880.4560.03250.0750.0921-0.0509-0.0388-0.0007-0.13430.0231-0.10710.11260.00090.00370.06720.00410.082-32.343-19.562817.0798
30.8898-0.3408-0.14270.484-0.13190.4093-0.00520.1182-0.0623-0.0402-0.04040.0629-0.0213-0.0998-0.01190.12140.012-0.01970.1198-0.00250.101-39.458-24.366515.8277
40.2544-0.09620.22940.35740.00670.23310.003-0.01850.34280.09920.0042-0.0231-0.07460.1259-0.00530.1253-0.0225-0.02150.13780.00270.1963-16.1677-14.429824.231
50.206-0.2253-0.00950.2852-0.13480.2174-0.0234-0.0571-0.1735-0.096-0.0511-0.21880.06140.0709-00.12320.00530.02560.1434-0.01760.1822-17.6856-38.942416.3805
60.1227-0.16010.10690.27580.03210.4719-0.19550.10530.0373-0.14130.1004-0.06050.0620.1191-0.00060.1316-0.00510.01730.12930.00370.1655-19.3764-38.271417.365
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 248 )
4X-RAY DIFFRACTION4chain 'A' and (resid 249 through 281 )
5X-RAY DIFFRACTION5chain 'L' and (resid 101 through 111 )
6X-RAY DIFFRACTION6chain 'M' and (resid 201 through 211 )

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