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

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Basic information

Entry
Database: PDB / ID: 5hlt
TitleCrystal structure of pyrene- and phenanthrene-modified DNA in complex with the BpuJ1 endonuclease binding domain
Components
  • DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
  • DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*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: 2.672 Å
AuthorsProbst, M. / Aeschimann, W. / Chau, T.-T.-H. / Langenegger, S.M. / Stocker, A. / Haener, R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationGrant 200020_149148 to RH Switzerland
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 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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
B: Restriction endonuclease R.BpuJI
L: DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
M: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')
C: DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
D: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')


Theoretical massNumber of molelcules
Total (without water)82,5516
Polymers82,5516
Non-polymers00
Water90150
1
A: Restriction endonuclease R.BpuJI
C: DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
D: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,2753
Polymers41,2753
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-22 kcal/mol
Surface area14760 Å2
MethodPISA
2
B: Restriction endonuclease R.BpuJI
L: DNA (5'-D(*GP*YPY*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')
M: DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')


Theoretical massNumber of molelcules
Total (without water)41,2753
Polymers41,2753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-20 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.870, 85.503, 115.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Restriction endonuclease R.BpuJI


Mass: 33766.219 Da / Num. of mol.: 2
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*TP*AP*CP*CP*CP*GP*TP*GP*GP*A)-3')


Mass: 3774.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*CP*AP*CP*GP*GP*GP*TP*AP*YPY*C)-3')


Mass: 3734.549 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Magnesium acetate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.672→46.491 Å / Num. obs: 40071 / % possible obs: 94.5 % / Redundancy: 1.79 % / CC1/2: 0.998 / Net I/σ(I): 12.89
Reflection shellResolution: 2.672→2.83 Å / Redundancy: 1.71 % / Mean I/σ(I) obs: 1.7 / % possible all: 89.5

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Processing

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

2vla


Resolution: 2.672→46.491 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.29 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2436 1990 4.97 %Random selection
Rwork0.2007 ---
obs0.203 40025 94.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.672→46.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 965 0 50 5417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035578
X-RAY DIFFRACTIONf_angle_d0.6097722
X-RAY DIFFRACTIONf_dihedral_angle_d17.8152073
X-RAY DIFFRACTIONf_chiral_restr0.024829
X-RAY DIFFRACTIONf_plane_restr0.004851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6725-2.73930.31231210.29842393X-RAY DIFFRACTION84
2.7393-2.81340.37411450.29592750X-RAY DIFFRACTION94
2.8134-2.89610.31411440.28732660X-RAY DIFFRACTION93
2.8961-2.98960.37261400.28842657X-RAY DIFFRACTION93
2.9896-3.09640.31021480.26732797X-RAY DIFFRACTION98
3.0964-3.22040.33211470.24442821X-RAY DIFFRACTION98
3.2204-3.36690.26311430.21242828X-RAY DIFFRACTION98
3.3669-3.54440.27281480.21542824X-RAY DIFFRACTION98
3.5444-3.76630.19231390.20172757X-RAY DIFFRACTION97
3.7663-4.0570.26011440.18132694X-RAY DIFFRACTION94
4.057-4.4650.24081390.16882651X-RAY DIFFRACTION92
4.465-5.11030.19231440.15932795X-RAY DIFFRACTION97
5.1103-6.43580.20561490.18522747X-RAY DIFFRACTION96
6.4358-46.49770.19791390.16692661X-RAY DIFFRACTION93
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)
15.132-4.49083.01055.7549-3.61964.96450.1127-0.062-0.5498-1.35310.26620.94070.3939-0.2776-0.32720.4359-0.08180.01490.5065-0.09490.446199.6014-6.0391115.8506
20.33950.98211.00823.6940.96025.8718-0.16960.24810.3961-0.40620.02760.8905-0.5263-0.59530.13910.42090.0452-0.12080.56570.08820.740888.359817.6054115.4184
30.0594-0.12060.45344.53120.42144.0110.015-0.01950.10140.13970.06030.6941-0.0895-0.0881-0.070.309-0.06150.0390.53610.01270.560492.55028.8976126.5215
46.5326-0.21812.63633.59410.13494.2171-0.15780.2692-0.2265-0.24030.0941-0.06390.57640.02520.02030.4388-0.06390.0310.351-0.03650.3822103.6248-10.6717123.5978
53.4731-1.6363.06334.0028-1.76332.49110.25630.2691-0.1665-0.3180.00950.31420.69130.1255-0.23490.4795-0.01710.02860.5266-0.0460.3822107.4885-9.6349115.6208
68.22840.13121.23382.8367-0.41042.26480.0402-0.366-0.38890.12380.0960.19810.3323-0.0384-0.07280.47520.00630.05550.3591-0.02750.4285101.2025-2.4901129.2823
76.4584-2.9173.26875.5842.85516.55820.5828-0.9479-0.27810.7199-0.41710.85850.4554-1.0473-0.21750.5196-0.08990.12940.65930.08230.831984.5531.5178128.4521
87.089-4.47763.52994.6291-5.35036.99970.40020.0976-0.35710.3548-0.11831.1145-0.16860.3977-0.29620.4463-0.0190.05120.557-0.02060.389899.697632.4768136.9925
92.5720.13120.68421.8912-1.1583.0329-0.2533-0.04320.55850.01760.10780.2678-0.5005-0.33620.11420.44630.0788-0.03680.492-0.05950.701989.550848.9682139.5601
106.1774-4.57765.2275.5663-4.10144.38020.3623-0.3810.2576-0.1579-0.0488-1.15610.38240.4686-0.24230.52260.0219-0.02730.4468-0.05730.4914110.358233.8596149.8774
113.51750.51771.841.88310.31312.41220.04830.1198-0.0157-0.01720.03880.07750.26870.2632-0.10020.41160.02070.02450.44780.00630.4141107.573428.7583139.3677
124.16030.65671.36717.33552.30911.1807-0.1111-0.3140.49410.03690.0803-0.2773-0.59320.4915-0.08820.46210.0475-0.080.5478-0.00740.5269110.902442.481148.6507
135.1267-3.00530.0052.28370.17173.73010.03320.1762-0.67390.4169-0.09620.6560.0366-0.7301-0.00720.39320.02180.14440.5718-0.05940.656885.062236.0151149.3326
141.2718-0.70450.23296.32321.42176.7088-0.7450.49630.3594-0.42470.1410.494-0.226-0.57580.25580.5521-0.0278-0.15770.66770.06620.7890.308939.4958125.1173
159.68132.35485.84263.11810.17784.5452-0.0434-0.01010.1619-0.1841-0.0530.31310.2515-0.13140.10020.56840.02270.07240.55550.08720.749490.833839.2877125.7818
160.0677-0.26610.63374.75720.78264.7833-0.30570.63250.5396-0.49670.14230.97350.1222-0.71970.20230.6362-0.1228-0.29430.80930.08820.845689.01892.1919105.2047
177.63744.91841.94167.51240.2627.3835-0.55620.6936-0.5032-0.99810.66931.58140.8329-0.5376-0.20910.8039-0.0726-0.21130.6946-0.0030.777690.36221.9907106.2006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 264 )
7X-RAY DIFFRACTION7chain 'A' and (resid 265 through 279 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 21 )
9X-RAY DIFFRACTION9chain 'B' and (resid 22 through 136 )
10X-RAY DIFFRACTION10chain 'B' and (resid 137 through 151 )
11X-RAY DIFFRACTION11chain 'B' and (resid 152 through 219 )
12X-RAY DIFFRACTION12chain 'B' and (resid 220 through 246 )
13X-RAY DIFFRACTION13chain 'B' and (resid 247 through 279 )
14X-RAY DIFFRACTION14chain 'L' and (resid 101 through 112 )
15X-RAY DIFFRACTION15chain 'M' and (resid 201 through 212 )
16X-RAY DIFFRACTION16chain 'C' and (resid 101 through 112 )
17X-RAY DIFFRACTION17chain 'D' and (resid 201 through 212 )

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