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- PDB-4esj: RESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA -

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Basic information

Entry
Database: PDB / ID: 4esj
TitleRESTRICTION ENDONUCLEASE DpnI IN COMPLEX WITH TARGET DNA
Components
  • DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
  • Type-2 restriction enzyme DpnI
KeywordsHYDROLASE/DNA / RESTRICTION ENDONUCLEASE-DNA COMPLEX / TYPE IIM / TYPE IIE / RESTRICTION ENZYME / DPNI / METHYLATION DEPENDENT / N6-METHYLADENINE / PD-(D/E)XK TYPE ENDONUCLEASE / WINGED HELIX DOMAIN / RESTRICTION ENDONUCLEASE / DNA BINDING / HYDROLASE-DNA complex
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Dam replacing family, catalytic PD-(D/E)XK domain / Dam-replacing / Dam-replacing protein, HTH domain / Dam replacing family, catalytic PD-(D/E)XK domain / Dam-replacing family / Dam-replacing HTH domain / PvuII Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily ...Dam replacing family, catalytic PD-(D/E)XK domain / Dam-replacing / Dam-replacing protein, HTH domain / Dam replacing family, catalytic PD-(D/E)XK domain / Dam-replacing family / Dam-replacing HTH domain / PvuII Endonuclease; Chain A / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / DNA / Type-2 restriction enzyme DpnI
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsSiwek, W. / Czapinska, H. / Bochtler, M. / Bujnicki, J.M. / Skowronek, K.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI.
Authors: Siwek, W. / Czapinska, H. / Bochtler, M. / Bujnicki, J.M. / Skowronek, K.
History
DepositionApr 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: Type-2 restriction enzyme DpnI
B: Type-2 restriction enzyme DpnI
C: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
E: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
F: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,72313
Polymers72,3936
Non-polymers3307
Water3,549197
1
A: Type-2 restriction enzyme DpnI
C: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
D: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4619
Polymers36,1963
Non-polymers2656
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type-2 restriction enzyme DpnI
E: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
F: DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2624
Polymers36,1963
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.518, 98.411, 83.884
Angle α, β, γ (deg.)90.00, 112.21, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

ZN

DetailsBIOLOGICAL UNIT CONTAINS A MONOMERIC PROTEIN AND DOUBLE STRANDED DNA FRAGMENT BOUND TO ITS C-TERMINAL WINGED HELIX DOMAIN (ASSEMBLY 1 COMPRISES CHAINS A,C,D; ASSEMBLY 2 COMPRISES CHAINS B,E,F). TO THE BEST OF OUR KNOWLEDGE ADDITIONAL COPY OF DOUBLE STRANDED TARGET DNA BINDS TO THE N-TERMINAL CATALYTIC DOMAIN OF THE ENZYME IN SOLUTION. THE TRIMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE MONOMERIC ENZYME WITH DOUBLE STRANDED DNA FRAGMENT PRESENT IN THE CRYSTAL

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Components

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Protein / DNA chain , 2 types, 6 molecules ABCDEF

#1: Protein Type-2 restriction enzyme DpnI / R.DpnI / Endonuclease DpnI / Type II restriction enzyme DpnI


Mass: 30078.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: dpnC, spr1665 / Plasmid: PET28 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2925
References: UniProt: P0A460, type II site-specific deoxyribonuclease
#2: DNA chain
DNA (5'-D(*CP*TP*GP*GP*(6MA)P*TP*CP*CP*AP*G)-3')


Mass: 3059.031 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic oligonucleotide

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Non-polymers , 5 types, 204 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 3.44 Å3/Da / Density % sol: 64.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 200 MM POTASSIUM SULFATE, 100 MM BETAINE, 20 % W/V PEG 3350, PH 6.8. FOR CRYOCOOLING THE CRYSTALLIZATION BUFFER WAS MIXED IN 3:1 RATIO WITH 100% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949,1.2833,1.2835
DetectorType: ADSC Q315 / Detector: CCD / Date: Dec 5, 2010 / Details: BENT MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
21.28331
31.28351
ReflectionResolution: 2.05→20 Å / Num. all: 60190 / Num. obs: 60190 / % possible obs: 98 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 17.5
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4429 / Rsym value: 0.3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXDEphasing
DMmodel building
ARP/wARPmodel building
REFMAC5.2.0019refinement
CNSrefinement
XDSdata reduction
SCALAdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→19.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: PROGRAM CNS HAS BEEN USED FOR DNA REFINEMENT. NO SUGAR PUCKER CONSTRAINTS HAVE BEEN APPLIED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.21754 3032 5 %RANDOM
Rwork0.19772 ---
all0.19872 60188 --
obs0.19872 60188 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.81 Å2
2---0.44 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4036 730 14 197 4977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225183
X-RAY DIFFRACTIONr_bond_other_d00.023449
X-RAY DIFFRACTIONr_angle_refined_deg1.242.1347150
X-RAY DIFFRACTIONr_angle_other_deg3.95438425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1125532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56824.518228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76815831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5031528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025311
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02997
X-RAY DIFFRACTIONr_nbd_refined0.1940.2895
X-RAY DIFFRACTIONr_nbd_other0.2460.23331
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22423
X-RAY DIFFRACTIONr_nbtor_other0.1090.22225
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2490.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2390.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.52581
X-RAY DIFFRACTIONr_mcbond_other01.51032
X-RAY DIFFRACTIONr_mcangle_it1.20124215
X-RAY DIFFRACTIONr_scbond_it1.73632602
X-RAY DIFFRACTIONr_scangle_it2.7254.52935
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 214 -
Rwork0.263 4178 -
obs-4392 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)
11.94331.44610.43692.27490.22790.9341-0.084-0.0124-0.0091-0.08520.0316-0.0923-0.14350.22810.0525-0.1902-0.0484-0.0602-0.08160.06310.057919.09620.674-5.28
24.02981.76850.36655.23410.32682.38160.2369-0.53740.01740.3173-0.12560.30420.3152-0.3396-0.1113-0.1977-0.1619-0.02520.00190.0255-0.000934.62939.1129.006
31.611.32961.64352.75220.98523.34250.1889-0.0567-0.21380.45160.0526-0.23630.19560.159-0.2415-0.1062-0.0012-0.1-0.085-0.01680.04923.79210.70828.681
45.77321.97560.18827.28772.8868.07940.6462-0.5814-0.16070.1442-0.1996-0.17010.30430.2283-0.4466-0.0147-0.2056-0.0573-0.0616-0.099-0.168413.03125.95150.08
52.60370.78380.18523.06450.11691.72880.03070.09090.05050.03080.0806-0.09190.1248-0.1587-0.1113-0.1827-0.0619-0.0312-0.044-0.06150.003745.348.5332.771
62.7575-0.1684-1.58127.65486.38969.8561-0.1073-0.00450.3431-0.6290.6961-0.7602-0.31770.3384-0.58880.0709-0.31510.11440.0876-0.1897-0.076420.2739.14152.213
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 182
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2A183 - 254
4X-RAY DIFFRACTION3B1 - 182
5X-RAY DIFFRACTION3B301
6X-RAY DIFFRACTION4B183 - 254
7X-RAY DIFFRACTION5C1 - 10
8X-RAY DIFFRACTION5D1 - 10
9X-RAY DIFFRACTION6E3 - 10
10X-RAY DIFFRACTION6F1 - 8

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