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- PDB-3fc3: Crystal structure of the beta-beta-alpha-Me type II restriction e... -

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Basic information

Entry
Database: PDB / ID: 3fc3
TitleCrystal structure of the beta-beta-alpha-Me type II restriction endonuclease Hpy99I
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 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / SH3 type barrels. - #140 / His-Me finger superfamily / 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: 1.75 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
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)52,76912
Polymers52,2444
Non-polymers5258
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11400 Å2
ΔGint-89 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.089, 90.089, 334.254
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsBiological 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, 402 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1. THE COORDINATION SPHERES PROVIDED AUTOMATICALLY AS REMARK 620 HAVE BEEN SKIPPED UPON AUTHOR'S ...1. THE COORDINATION SPHERES PROVIDED AUTOMATICALLY AS REMARK 620 HAVE BEEN SKIPPED UPON AUTHOR'S REQUEST BECAUSE THESE RECORDS MAKE A FALSE IMPRESSION THAT THE SODIUM IS OCTA-COORDINATED. THE CORRECT RECORDS ARE PROVIDED IN THE MMCIF FILE IN CATEGORY _DATABASE_PDB_REMARK. 2. THE LINK RECORDS THAT INVOLVE ZN AND NA IONS HAVE BEEN REMOVED UPON AUTHOR'S REQUEST.

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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: 2.5 Å3/Da / Density % sol: 50.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES/Sodium hydroxide pH 6.5, 0.1 M Sodium chloride, 0.1 M Lithium sulfate, 30 % PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES11
2Sodium hydroxide11
3Sodium chloride11
4Lithium sulfate11
5PEG 40011
6MES12
7Sodium hydroxide12
8Sodium chloride12
9Lithium sulfate12
10PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97982 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 8, 2008
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. all: 51564 / Num. obs: 51564 / % possible obs: 96.8 % / Redundancy: 3.99 % / Biso Wilson estimate: 22.6 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.52
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.95 % / Mean I/σ(I) obs: 4.48 / Num. unique all: 3874 / Rsym value: 0.4 / % possible all: 99.1

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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: 1.75→19.71 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 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
Rfree0.20533 2654 5.1 %RANDOM
Rwork0.18084 ---
all0.18212 51564 --
obs0.18212 51564 96.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.338 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 363 20 394 3751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223935
X-RAY DIFFRACTIONr_bond_other_d00.022541
X-RAY DIFFRACTIONr_angle_refined_deg1.2242.1995453
X-RAY DIFFRACTIONr_angle_other_deg3.91736247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99624.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15415598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8121521
X-RAY DIFFRACTIONr_chiral_restr0.0770.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023866
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02677
X-RAY DIFFRACTIONr_nbd_refined0.2050.2618
X-RAY DIFFRACTIONr_nbd_other0.2380.22291
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21754
X-RAY DIFFRACTIONr_nbtor_other0.1060.21565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.29
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0660.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.51925
X-RAY DIFFRACTIONr_mcbond_other01.5790
X-RAY DIFFRACTIONr_mcangle_it1.26323130
X-RAY DIFFRACTIONr_scbond_it1.74532010
X-RAY DIFFRACTIONr_scangle_it2.6624.52323
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
Rfree0.251 185 -
Rwork0.234 3657 -
obs-3842 99.05 %
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)
11.1687-0.4824-0.17772.49-0.53552.05440.02280.0612-0.0263-0.13720.0107-0.12220.08720.1593-0.0335-0.04270.018-0.0071-0.0691-0.0164-0.01352.65416.229114.446
20.8766-0.5012-0.84850.74940.98991.3717-0.1307-0.1114-0.05680.10590.0933-0.01050.23830.2180.03740.01420.0268-0.0139-0.07720.0029-0.0296-8.54115.134134.469
30.2477-0.3117-0.15040.40910.33041.27170.1197-0.22710.1738-0.05260.0999-0.0701-0.23830.2488-0.21950.0257-0.04180.03450.0098-0.0703-0.0216-9.91735.179144.17
42.74440.56450.99570.76660.38462.1184-0.0378-0.1890.11690.1184-0.02360.0477-0.0724-0.16760.06140.01450.01580.00550.008-0.0193-0.0241-34.88441.309164.546
51.4182-0.2256-1.45750.60180.26991.50050.07760.064-0.0260.0113-0.11840.0639-0.0669-0.33620.0408-0.0030.0127-0.00820.0149-0.0173-0.0169-31.57429.973144.372
60.67850.006-0.27280.3470.45351.41560.2055-0.03580.1469-0.1489-0.0382-0.1251-0.3543-0.0334-0.16730.08040.00890.06-0.0898-0.0166-0.0263-13.21236.944134.113
71.071-0.5818-0.5880.56970.38531.9216-0.033-0.045-0.11680.064-0.00310.06630.0439-0.0940.0361-0.0422-0.00290.0105-0.0923-0.0145-0.0673-19.38723.525139.532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 54
2X-RAY DIFFRACTION2A55 - 113
3X-RAY DIFFRACTION3A134 - 188
4X-RAY DIFFRACTION4B2 - 54
5X-RAY DIFFRACTION5B55 - 113
6X-RAY DIFFRACTION6B134 - 188
7X-RAY DIFFRACTION7C-4 - 4
8X-RAY DIFFRACTION7D-4 - 4

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