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- PDB-4pxg: Crystal Structure of TypeII restriction Enzyme Sau3AI -

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Basic information

Entry
Database: PDB / ID: 4pxg
TitleCrystal Structure of TypeII restriction Enzyme Sau3AI
ComponentsType-2 restriction enzyme Sau3AI
KeywordsHYDROLASE / Type II restriction enzyme
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 / SAD / Resolution: 2.45 Å
AuthorsXu, C.Y. / Yu, F. / Hu, X.J. / He, J.H.
CitationJournal: To be Published
Title: The 2.45 A Crystal Structure of the Restriction Endonuclease Sau3AI Suggests a Self-Inhibition Mechanism
Authors: Xu, C.Y. / Yu, F. / Hu, X.J. / He, J.H.
History
DepositionMar 24, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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

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Assembly

Deposited unit
A: Type-2 restriction enzyme Sau3AI
B: Type-2 restriction enzyme Sau3AI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,2183
Polymers118,1782
Non-polymers401
Water55831
1
A: Type-2 restriction enzyme Sau3AI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1292
Polymers59,0891
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Type-2 restriction enzyme Sau3AI


Theoretical massNumber of molelcules
Total (without water)59,0891
Polymers59,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.648, 197.673, 191.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 6 - 489 / Label seq-ID: 26 - 509

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Type-2 restriction enzyme Sau3AI / R.Sau3AI / Endonuclease Sau3AI / Type II restriction enzyme Sau3AI


Mass: 59089.082 Da / Num. of mol.: 2 / Mutation: E64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: 3A / Gene: sau3AIR / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: P16667, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 16% polyethylene glycol 8000, 1M sodium acetate, 0.2M calcium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9789
SYNCHROTRONSSRF BL17U20.9792
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJul 7, 2007
ADSC QUANTUM 315r2CCDJun 22, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97921
ReflectionResolution: 2.45→54.14 Å / Num. all: 47905 / Num. obs: 47905 / % possible obs: 8.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.6 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.45-2.684.10.3313.5105110.40924.3
6-54.1412.90.03670.943930.0397.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.307 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.432 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26331 2331 5.1 %RANDOM
Rwork0.22373 ---
obs0.22576 43797 94.07 %-
all-46127 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å20 Å2
2---6.97 Å2-0 Å2
3---6.56 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7608 0 1 31 7640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197778
X-RAY DIFFRACTIONr_bond_other_d0.0040.027369
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.95310471
X-RAY DIFFRACTIONr_angle_other_deg0.95317071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5625.389386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.358151430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6351528
X-RAY DIFFRACTIONr_chiral_restr0.0810.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028715
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4186.9013718
X-RAY DIFFRACTIONr_mcbond_other5.4176.9013717
X-RAY DIFFRACTIONr_mcangle_it8.15610.3414637
X-RAY DIFFRACTIONr_mcangle_other8.15510.3414638
X-RAY DIFFRACTIONr_scbond_it5.8957.3424059
X-RAY DIFFRACTIONr_scbond_other5.8957.3424059
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.01410.7495834
X-RAY DIFFRACTIONr_long_range_B_refined11.77453.8278699
X-RAY DIFFRACTIONr_long_range_B_other11.77453.838700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 28575 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.449→2.512 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 111 -
Rwork0.396 1964 -
obs--58.06 %

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