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- PDB-2ixs: Structure of SdaI restriction endonuclease -

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Basic information

Entry
Database: PDB / ID: 2ixs
TitleStructure of SdaI restriction endonuclease
ComponentsSDAI RESTRICTION ENDONUCLEASE
KeywordsHYDROLASE / RESTRICTION ENDONUCLEASE / SDAI / ENDONUCLEASE / DOMAIN ARCHITECTURE
Function / homology
Function and homology information


type II site-specific deoxyribonuclease activity / DNA restriction-modification system / magnesium ion binding / DNA binding
Similarity search - Function
BsuBI/PstI restriction endonuclease, N-terminal domain / BsuBI/PstI restriction endonuclease, C-terminal domain / BsuBI/PstI restriction endonuclease domain / BsuBI/PstI restriction endonuclease, HTH domain / BsuBI/PstI restriction endonuclease, N-terminal domain superfamily / BsuBI/PstI restriction endonuclease, C-terminal domain superfamily / BsuBI/PstI restriction endonuclease domain / BsuBI/PstI restriction endonuclease HTH domain / Trna Endonuclease; Chain: A, domain 1 / Arc Repressor Mutant, subunit A ...BsuBI/PstI restriction endonuclease, N-terminal domain / BsuBI/PstI restriction endonuclease, C-terminal domain / BsuBI/PstI restriction endonuclease domain / BsuBI/PstI restriction endonuclease, HTH domain / BsuBI/PstI restriction endonuclease, N-terminal domain superfamily / BsuBI/PstI restriction endonuclease, C-terminal domain superfamily / BsuBI/PstI restriction endonuclease domain / BsuBI/PstI restriction endonuclease HTH domain / Trna Endonuclease; Chain: A, domain 1 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTREPTOMYCES DIASTATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2 Å
AuthorsTamulaitiene, G. / Jakubauskas, A. / Urbanke, C. / Huber, R. / Grazulis, S. / Siksnys, V.
CitationJournal: Structure / Year: 2006
Title: The Crystal Structure of the Rare-Cutting Restriction Enzyme Sdai Reveals Unexpected Domain Architecture
Authors: Tamulaitiene, G. / Jakubauskas, A. / Urbanke, C. / Huber, R. / Grazulis, S. / Siksnys, V.
History
DepositionJul 11, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SDAI RESTRICTION ENDONUCLEASE
B: SDAI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,63815
Polymers73,0532
Non-polymers1,58513
Water8,467470
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A: SDAI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3678
Polymers36,5261
Non-polymers8417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SDAI RESTRICTION ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2717
Polymers36,5261
Non-polymers7456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.901, 237.991, 111.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsALTHOUGH SDAI IS A DIMER, NO BIOLOGICALLY RELEVANT DIMERCAN BE CONSTRUCTED IN THE PRESENT STRUCTURE, WHICH ISTHE REASON THIS ENTRY IS MARKED AS MONOMERIC.

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Components

#1: Protein SDAI RESTRICTION ENDONUCLEASE


Mass: 36526.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES DIASTATICUS (bacteria) / Strain: NG7-324 / Plasmid: PAL-SDAIR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2267
References: UniProt: C4P954*PLUS, type II site-specific deoxyribonuclease
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.04 Å3/Da / Density % sol: 59.2 %
Description: HGCL2 DERIVATIVE WAS USED FOR THE SIRAS EXPERIMENT
Crystal growpH: 7.5 / Details: 1.7-2.0 M (NH4)2SO4, 0.1 M NA-HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9755
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 9, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2→51.2 Å / Num. obs: 60505 / % possible obs: 100 % / Observed criterion σ(I): 1.4 / Redundancy: 7.4 % / Biso Wilson estimate: 19.03 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.229 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.REFINEMENT WAS CONDUCTED WITH CNS, FINAL STEPS OF REFINEMENT WERE MADE WITH REFMAC. RESIDUES 1-4 ARE DISORDERED. SDAI IS A DIMER IN SOLUTION ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.REFINEMENT WAS CONDUCTED WITH CNS, FINAL STEPS OF REFINEMENT WERE MADE WITH REFMAC. RESIDUES 1-4 ARE DISORDERED. SDAI IS A DIMER IN SOLUTION HOWEVER WE COULD NOT IDENTIFY BIOLOGICALLY RELEVANT DIMER IN THE CRYSTAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 6068 10 %RANDOM
Rwork0.178 ---
obs0.182 54406 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5090 0 91 470 5651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215364
X-RAY DIFFRACTIONr_bond_other_d00.024812
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.9587286
X-RAY DIFFRACTIONr_angle_other_deg0.761311159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5835652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025983
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021158
X-RAY DIFFRACTIONr_nbd_refined0.2220.21143
X-RAY DIFFRACTIONr_nbd_other0.2710.25601
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0890.23067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2351
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.236
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.2145
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0951.53238
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.20325194
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.71632126
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.8254.52092
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 409
Rwork0.203 3995

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