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- PDB-3gox: Crystal structure of the beta-beta-alpha-Me type II restriction e... -

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Basic information

Entry
Database: PDB / ID: 3gox
TitleCrystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I in the absence of EDTA
Components
  • 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'
  • 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'
  • Restriction endonuclease Hpy99I
KeywordsHYDROLASE/DNA / ENDONUCLEASE-DNA COMPLEX / RESTRICTION ENZYME / HPY99I / PSEUDOPALINDROME / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


Wheat Germ Agglutinin (Isolectin 2); domain 1 - #130 / Restriction endonuclease, SH3 domain / His-Me finger endonuclease, beta4-alpha2 domain / His-Me finger endonuclease beta4-alpha2 domain / Restriction endonuclease SH3 domain / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold ...Wheat Germ Agglutinin (Isolectin 2); domain 1 - #130 / Restriction endonuclease, SH3 domain / His-Me finger endonuclease, beta4-alpha2 domain / His-Me finger endonuclease beta4-alpha2 domain / Restriction endonuclease SH3 domain / His-Me finger endonucleases / Recombination endonuclease VII / Recombination endonuclease VII superfamily / Recombination endonuclease VII / His-Me finger endonuclease fold / His-Me finger superfamily / Wheat Germ Agglutinin (Isolectin 2); domain 1 / SH3 type barrels. - #140 / SH3 type barrels. / Roll / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSokolowska, M. / Czapinska, H. / Bochtler, M.
Citation
Journal: Nucleic Acids Res. / Year: 2009
Title: Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA.
Authors: Sokolowska, M. / Czapinska, H. / Bochtler, M.
#1: Journal: Nature / Year: 2007
Title: Crystal structure of T4 endonuclease VII resolving a Holliday junction.
Authors: Biertumpfel, C. / Yang, W. / Suck, D.
#2: Journal: Nature / Year: 1998
Title: DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Authors: Flick, K.E. / Jurica, M.S. / Monnat, R.J. / Stoddard, B.L.
History
DepositionMar 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq / 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_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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

Downloads & links

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Assembly

Deposited unit
A: Restriction endonuclease Hpy99I
B: Restriction endonuclease Hpy99I
C: 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'
D: 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,81312
Polymers52,2444
Non-polymers5698
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-57.6 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.682, 90.682, 334.933
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsTHE 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.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Restriction endonuclease Hpy99I


Mass: 22768.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic gene (NCBI-GeneID:890139) codon optimized for Escherichia coli
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: J99
Gene: jhp_0755, synthetic gene codon optimized for Escherichia coli
Plasmid: pET15bmod / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q9ZL26

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain 5'-(*DCP*DTP*DCP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DA)-3'


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain 5'-(*DTP*DAP*DCP*DGP*DTP*DCP*DGP*DAP*DGP*DTP*DC)-3'


Mass: 3349.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA

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Non-polymers , 4 types, 484 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/Sodium hydroxide pH 7.5, 0.1 M Sodium chloride, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1HEPES/Sodium hydroxide11
2Sodium chloride11
3PEG 40011
4HEPES/Sodium hydroxide12
5Sodium chloride12
6PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 23, 2008
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 84393 / Num. obs: 84393 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.04 / Net I/σ(I): 16.62
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.57 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.335 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→19.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Program CNS (AUTHORS: BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN) has been used for DNA refinement. No sugar pucker constraints ...Details: Program CNS (AUTHORS: BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE,SIMONSON,WARREN) 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
Rfree0.18639 4298 5.1 %RANDOM
Rwork0.16873 ---
obs0.16964 84392 99.64 %-
all-84392 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 405 23 476 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224073
X-RAY DIFFRACTIONr_bond_other_d00.022613
X-RAY DIFFRACTIONr_angle_refined_deg1.2072.2155658
X-RAY DIFFRACTIONr_angle_other_deg3.9536427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84924.648142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66115606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2461520
X-RAY DIFFRACTIONr_chiral_restr0.080.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023954
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02692
X-RAY DIFFRACTIONr_nbd_refined0.2030.2622
X-RAY DIFFRACTIONr_nbd_other0.2360.22223
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21780
X-RAY DIFFRACTIONr_nbtor_other0.1070.21503
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2329
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.211
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3360.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6261.51955
X-RAY DIFFRACTIONr_mcbond_other01.5803
X-RAY DIFFRACTIONr_mcangle_it1.17123179
X-RAY DIFFRACTIONr_scbond_it1.69332118
X-RAY DIFFRACTIONr_scangle_it2.6634.52479
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 322 -
Rwork0.229 5839 -
obs--99.9 %
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)
11.3769-0.3919-0.25052.4606-0.65791.91770.02750.0879-0.0665-0.1557-0.0059-0.1380.14720.1625-0.0216-0.01160.0132-0.0028-0.0262-0.0161-0.06092.66416.294114.421
21.2681-0.151-0.84991.36771.08711.8346-0.1114-0.0662-0.09020.12310.00930.09970.22120.08140.1020.02540.01330.01-0.059-0.0015-0.0626-9.55914.196132.447
30.7474-0.4392-0.50310.55010.63751.44860.0598-0.23870.1442-0.05290.1646-0.1199-0.13140.3489-0.2244-0.0124-0.03850.02010.0568-0.0604-0.0558-9.92833.97148.722
42.56680.26010.81990.70130.55752.1007-0.0202-0.18910.120.0725-0.01770.0578-0.0284-0.12610.0379-0.017-0.0011-0.0003-0.0144-0.0096-0.0648-35.11441.504164.994
51.4135-0.0097-1.27731.52790.14051.5029-0.00840.0967-0.1294-0.0344-0.06280.0240.0309-0.15460.0712-0.0209-0.0134-0.005-0.0063-0.0082-0.0599-32.21128.748147.268
60.902-0.318-0.73680.61260.43051.92640.2530.07510.181-0.1594-0.0645-0.0652-0.4381-0.0991-0.18840.09170.02760.0608-0.05020.008-0.057-14.64836.498130.189
71.7227-0.8586-0.86290.82330.72692.135-0.04170.0121-0.19010.0318-0.03720.12580.1311-0.0870.07890.0319-0.01170.0226-0.0054-0.0196-0.0253-19.74823.329139.823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 54
2X-RAY DIFFRACTION2A55 - 106
3X-RAY DIFFRACTION3A107 - 190
4X-RAY DIFFRACTION4B1 - 54
5X-RAY DIFFRACTION5B55 - 106
6X-RAY DIFFRACTION6B107 - 190
7X-RAY DIFFRACTION7C-4 - 6
8X-RAY DIFFRACTION7D-4 - 6

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