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- PDB-3oqg: Restriction endonuclease HPY188I in complex with substrate DNA -

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Basic information

Entry
Database: PDB / ID: 3oqg
TitleRestriction endonuclease HPY188I in complex with substrate DNA
Components
  • DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'
  • DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'
  • Hpy188I
KeywordsHYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / HPY188I / INTERCALATION / GIY-YIG NUCLEASE / CATALYTIC MECHANISM / PSEUDOPALINDROME / HYDROLASE-DNA COMPLEX
Function / homologyGIY-YIG endonuclease - #50 / GIY-YIG endonuclease / endonuclease activity / 3-Layer(aba) Sandwich / Alpha Beta / DNA / GIY-YIG nuclease family protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsSokolowska, M. / Czapinska, H. / Bochtler, M.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.
Authors: Sokolowska, M. / Czapinska, H. / Bochtler, M.
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Remark 300BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C AND D. THE TETRAMER (ACCORDING TO ...BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C AND D. THE TETRAMER (ACCORDING TO PDB CONVENTIONS) IS A COMPLEX OF THE DIMERIC RESTRICTION ENZYME WITH ITS SUBSTRATE, DOUBLE STRANDED DNA. THE NATURAL PROTEIN OLIGOMERIZATION STATE IS A DIMER - THE DNA IS A SUBSTRATE. UNDER THE PHYSIOLOGICAL CONDITIONS THE PROTEIN DIMER BINDS DOUBLE STRANDED DNA AND CLEAVES IT TO TWO DOUBLE STRANDED DNA FRAGMENTS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hpy188I
B: Hpy188I
C: DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'
D: DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8127
Polymers47,7314
Non-polymers813
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-73 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.236, 65.236, 220.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hpy188I


Mass: 21130.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 188 / Gene: hpy188IR / Plasmid: PET15BMOD / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9KJ88

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA 5'-D(*GP*AP*TP*CP*TP*GP*AP*AP*C)-3'


Mass: 2739.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE
#3: DNA chain DNA 5'-D(*GP*TP*TP*CP*AP*GP*AP*TP*C)-3'


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE

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Non-polymers , 3 types, 362 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M MES/NaOH pH 6.2 and 30% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2010 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 48330 / Num. obs: 48330 / % possible obs: 98 % / Redundancy: 5.55 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 24.651
Reflection shellResolution: 1.75→1.77 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.265 / Num. unique all: 1895 / Rsym value: 0.44 / % possible all: 97.1

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Processing

Software
NameVersionClassification
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→19.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE DENSITY FOR THE NUCLEOPHILIC WATER MOLECULES (RESIDUES A173 & B172) IS VERY WEAK. IT MIGHT CORRESPOND TO A (HALF OCCUPIED) WATER MOLECULE OR A HYDROXIDE ION. ACCORDING TO THE MS DATA, ...Details: THE DENSITY FOR THE NUCLEOPHILIC WATER MOLECULES (RESIDUES A173 & B172) IS VERY WEAK. IT MIGHT CORRESPOND TO A (HALF OCCUPIED) WATER MOLECULE OR A HYDROXIDE ION. ACCORDING TO THE MS DATA, THE SELENOMETHIONINE SUBSTITUTION WAS SUCCESSFUL ONLY IN PART. THEREFORE, ONLY MET56 WAS MODELED AS SELENOMETHIONINE. HOWEVER, ALL THREE MET POSITIONS ARE LIKELY TO BE PARTIALLY OCCUPIED BY MET AND PARTIALLY BY MSE.THE CNS PROGRAM 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
Rfree0.19218 2393 5 %RESOLUTION SHELLS
Rwork0.16474 ---
all0.16612 48287 --
obs0.16612 48287 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 363 3 359 3619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224222
X-RAY DIFFRACTIONr_bond_other_d00.022657
X-RAY DIFFRACTIONr_angle_refined_deg1.2242.1725906
X-RAY DIFFRACTIONr_angle_other_deg3.96136612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585445
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22226.057175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09415667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.779158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024353
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02745
X-RAY DIFFRACTIONr_nbd_refined0.2080.2793
X-RAY DIFFRACTIONr_nbd_other0.230.22450
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21960
X-RAY DIFFRACTIONr_nbtor_other0.1120.21536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1560.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.28
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.239
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.61.52036
X-RAY DIFFRACTIONr_mcbond_other01.5801
X-RAY DIFFRACTIONr_mcangle_it1.10723387
X-RAY DIFFRACTIONr_scbond_it1.49232186
X-RAY DIFFRACTIONr_scangle_it2.2514.52514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 216 -
Rwork0.228 3222 -
obs-3438 97 %
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)
10.09170.01920.33071.08320.01891.19440.0103-0.014-0.0083-0.0347-0.0140.0090.06260.01670.0038-0.0631-0.0025-0.010.0048-0.012-0.0250.45515.75182.663
20.3773-0.1890.37690.8053-0.20431.45910.0357-0.06570.00440.0035-0.01070.08940.1067-0.1489-0.025-0.0692-0.0242-0.01010.0341-0.0154-0.0381-0.06812.05798.17
30.770.12040.38220.86960.38291.20980.03390.1408-0.00480.01540.0268-0.03870.03460.1211-0.0607-0.07790.003-0.0220.0461-0.0093-0.06010.8610.96667.39
44.25130.04831.10163.66810.27656.0910.07790.0026-0.45320.09110.07710.02031.04110.0084-0.1550.2383-0.0031-0.109-0.1078-0.0099-0.00040.159-7.62483.461
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C-4 - 4
2X-RAY DIFFRACTION1D-4 - 4
3X-RAY DIFFRACTION2A-9 - 127
4X-RAY DIFFRACTION2B143 - 170
5X-RAY DIFFRACTION3B-9 - 127
6X-RAY DIFFRACTION3A143 - 170
7X-RAY DIFFRACTION4A128 - 142
8X-RAY DIFFRACTION4B128 - 142

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