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- PDB-3or3: Restriction endonuclease HPY188I in complex with product DNA -

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Basic information

Entry
Database: PDB / ID: 3or3
TitleRestriction endonuclease HPY188I in complex with product DNA
Components
  • 5'-D(*GP*AP*TP*CP*T)-3'
  • 5'-D(*GP*TP*TP*CP*A)-3'
  • 5'-D(P*GP*AP*AP*C)-3'
  • 5'-D(P*GP*AP*TP*C)-3'
  • RESTRICTION ENDONUCLEASE HPY188I
KeywordsHYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / HPY188I / INTERCALATION / GIY-YIG NUCLEASE / CATALYTIC MECHANISM / PSEUDOPALINDROME / HYDROLASE-DNA COMPLEX / restriction endonuclease / DNA
Function / homologyGIY-YIG endonuclease - #50 / GIY-YIG endonuclease / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / DNA / Hpy188I
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 6, 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 / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C/E (DNA STRAND T CLEAVED) AND DNA ...BIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, DNA STRANDS C/E (DNA STRAND T CLEAVED) AND DNA STRANDS D/E (DNA STRAND A CLEAVED). THE HEXAMER (ACCORDING TO THE PDB CONVENTIONS) IS A COMPLEX OF THE DIMERIC RESTRICTION ENZYME WITH ITS PRODUCTS, TWO DOUBLE STRANDED DNA FRAGMENTS. THE NATURAL PROTEIN OLIGOMERIZATION STATE IS A DIMER - THE DNA IS A PRODUCT. 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: RESTRICTION ENDONUCLEASE HPY188I
B: RESTRICTION ENDONUCLEASE HPY188I
C: 5'-D(*GP*AP*TP*CP*T)-3'
D: 5'-D(*GP*TP*TP*CP*A)-3'
E: 5'-D(P*GP*AP*AP*C)-3'
F: 5'-D(P*GP*AP*TP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,90313
Polymers47,6416
Non-polymers2627
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11740 Å2
ΔGint-139 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.395, 65.395, 221.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-222-

HOH

21B-260-

HOH

DetailsBIOLOGICAL UNIT CONTAINS PROTEIN CHAINS A AND B, AND 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.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RESTRICTION ENDONUCLEASE 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, SYNTHETIC GENE CODON OPTIMIZED FOR ESCHERICHIA COLI
Plasmid: PET15BMOD / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9KJ88

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DNA chain , 4 types, 4 molecules CDEF

#2: DNA chain 5'-D(*GP*AP*TP*CP*T)-3'


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE
#3: DNA chain 5'-D(*GP*TP*TP*CP*A)-3'


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE
#4: DNA chain 5'-D(P*GP*AP*AP*C)-3'


Mass: 1199.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE
#5: DNA chain 5'-D(P*GP*AP*TP*C)-3'


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC OLIGONUCLEOTIDE

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Non-polymers , 3 types, 318 molecules

#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M MES/NaOH pH 6.2 and 30% MPD. CRYSTAL WAS SOAKED IN 0.1 M CaCl2 FOR 18 H., 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: 1.281 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 11, 2010 / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.281 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 35348 / Num. obs: 35348 / % possible obs: 97.5 % / Redundancy: 13.99 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 37.775
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 14.78 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 6.488 / Num. unique all: 1348 / Rsym value: 0.406 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MAR345data collection
ARP/wARPmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OQG

3oqg


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / SU B: 6.401 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 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 ...Details: 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
Rfree0.20144 1723 4.9 %RESOLUTION SHELLS
Rwork0.16849 ---
all0.17013 35323 --
obs0.17013 35323 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.527 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2844 365 7 311 3527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224158
X-RAY DIFFRACTIONr_bond_other_d00.022639
X-RAY DIFFRACTIONr_angle_refined_deg1.2812.1835809
X-RAY DIFFRACTIONr_angle_other_deg3.94336573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88826.213169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62215668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.47158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024258
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02728
X-RAY DIFFRACTIONr_nbd_refined0.1950.2748
X-RAY DIFFRACTIONr_nbd_other0.2320.22447
X-RAY DIFFRACTIONr_nbtor_refined0.190.21951
X-RAY DIFFRACTIONr_nbtor_other0.1120.21515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2310.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6731.52000
X-RAY DIFFRACTIONr_mcbond_other01.5787
X-RAY DIFFRACTIONr_mcangle_it1.18223323
X-RAY DIFFRACTIONr_scbond_it1.55132158
X-RAY DIFFRACTIONr_scangle_it2.1614.52479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.054 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 213 -
Rwork0.185 4717 -
obs-3298 96.1 %
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)
11.04490.00390.48250.81380.03051.3520.0107-0.0147-0.0078-0.00160.01340.02480.07310.0294-0.0241-0.0679-0.0033-0.00550.0188-0.0041-0.04330.17315.71783.189
21.0129-0.20850.45260.8648-0.23411.77260.0317-0.2067-0.047-0.01480.08390.09210.124-0.1568-0.1156-0.0973-0.0059-0.01560.05320.0128-0.0558-0.37511.97998.766
31.04430.06010.4530.86210.46611.64680.06020.1867-0.04260.03430.0523-0.02390.09970.1467-0.1126-0.09010.0056-0.03020.0464-0.022-0.06520.56911.00667.827
42.8549-0.42840.03822.02910.93427.0090.1069-0.0272-0.62380.090.17990.10341.3767-0.0146-0.28680.2733-0.0139-0.1656-0.15160.02010.0359-0.289-7.72583.889
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C-4 - 0
2X-RAY DIFFRACTION1D-4 - 0
3X-RAY DIFFRACTION1E1 - 4
4X-RAY DIFFRACTION1F1 - 4
5X-RAY DIFFRACTION2A-9 - 127
6X-RAY DIFFRACTION2B143 - 170
7X-RAY DIFFRACTION3B-9 - 127
8X-RAY DIFFRACTION3A143 - 170
9X-RAY DIFFRACTION4A128 - 142
10X-RAY DIFFRACTION4B128 - 142

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