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- PDB-2reu: Crystal Structure of the C-terminal of Sau3AI fragment -

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Basic information

Entry
Database: PDB / ID: 2reu
TitleCrystal Structure of the C-terminal of Sau3AI fragment
ComponentsType II restriction enzyme Sau3AI
KeywordsHYDROLASE / helix / beta / random coil / Endonuclease / Magnesium / Nuclease / Restriction system
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
DNA mismatch repair MutH/Type II restriction enzyme Sau3AI / DNA mismatch repair enzyme MutH / DNA mismatch repair enzyme MutH / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / Restriction endonuclease type II-like
Similarity search - Domain/homology
Type II restriction enzyme Sau3AI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsHu, X. / Yu, F. / Xu, C. / He, J.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Crystal structure and function of C-terminal Sau3AI domain
Authors: Xu, C.Y. / Yu, F. / Xu, S.J. / Ding, Y. / Sun, L.H. / Tang, L. / Hu, X.J. / Zhang, Z.H. / He, J.H.
History
DepositionSep 27, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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

Downloads & links

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Assembly

Deposited unit
A: Type II restriction enzyme Sau3AI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4182
Polymers30,3931
Non-polymers241
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.789, 122.009, 34.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Type II restriction enzyme Sau3AI / Endonuclease Sau3AI / R.Sau3AI


Mass: 30393.297 Da / Num. of mol.: 1 / Fragment: C-terminal fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sau3AIR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plysS
References: UniProt: P16667, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% iso-propanol, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9789, 0.97945, 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 7, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.979451
30.91
ReflectionAv σ(I) over netI: 10 / Number: 302170 / Rmerge(I) obs: 0.071 / Χ2: 1.03 / D res high: 1.9 Å / D res low: 30 Å / Num. obs: 25678 / % possible obs: 96.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
1.91.9777.110.4330.326
1.972.0594.110.3530.305
2.052.1498.310.2810.368
2.142.2598.210.2220.419
2.252.3998.710.170.485
2.392.5898.910.140.577
2.582.8499.210.0990.799
2.843.2599.610.071.138
3.254.0999.910.0511.691
4.093099.810.0472.766
ReflectionResolution: 1.9→30 Å / Num. obs: 25678 / % possible obs: 96.4 % / Rmerge(I) obs: 0.071 / Χ2: 1.034 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.970.43320150.326177.1
1.97-2.050.35324730.305194.1
2.05-2.140.28125430.368198.3
2.14-2.250.22225800.419198.2
2.25-2.390.1725960.485198.7
2.39-2.580.1426090.577198.9
2.58-2.840.09926300.799199.2
2.84-3.250.0726591.138199.6
3.25-4.090.05127111.691199.9
4.09-300.04728622.766199.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97942.61-10.43
13 wavelength20.97895.76-5.41
13 wavelength30.93.67-1.05
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se21.3720.2470.1750.231.072
2Se22.1060.6960.2670.1160.997
3Se21.9970.6760.2020.2540.839
4Se30.7860.7590.1570.0750.798

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.35 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.146 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1276 5 %RANDOM
Rwork0.199 ---
obs0.201 25634 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.739 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2--1.61 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1961 0 1 225 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222275
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.9383121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8835307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60625.588136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92915448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4591511
X-RAY DIFFRACTIONr_chiral_restr0.080.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021815
X-RAY DIFFRACTIONr_nbd_refined0.2250.31023
X-RAY DIFFRACTIONr_nbtor_refined0.3210.51532
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.5328
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.323
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.528
X-RAY DIFFRACTIONr_mcbond_it0.82421331
X-RAY DIFFRACTIONr_mcangle_it1.30432134
X-RAY DIFFRACTIONr_scbond_it0.71221085
X-RAY DIFFRACTIONr_scangle_it1.0263949
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 65 -
Rwork0.294 1348 -
all-1413 -
obs--72.42 %

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