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- PDB-5a0m: THE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN... -

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Basic information

Entry
Database: PDB / ID: 5a0m
TitleTHE CRYSTAL STRUCTURE OF I-SCEI IN COMPLEX WITH ITS TARGET DNA IN THE PRESENCE OF MN
Components
  • (INTRON-ENCODED ENDONUCLEASE I- ...) x 2
  • 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
  • 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
  • 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
  • 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / GENE TARGETING / GENETICS / PROTEIN-DNA INTERACTION / HOMING ENDONUCLEASES
Function / homology
Function and homology information


intron homing / RNA splicing / mRNA processing / endonuclease activity / Hydrolases; Acting on ester bonds / mitochondrion
Similarity search - Function
: / LAGLIDADG DNA endonuclease family / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Intron-encoded endonuclease I-SceI
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPrieto, J. / Redondo, P. / Merino, N. / Villate, M. / Blanco, F.J. / Molina, R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of the I-Scei Nuclease Complexed with its DsDNA Target and Three Catalytic Metal Ions.
Authors: Prieto, J. / Redondo, P. / Merino, N. / Villate, M. / Montoya, G. / Blanco, F.J. / Molina, R.
History
DepositionApr 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 29, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: INTRON-ENCODED ENDONUCLEASE I-SCEI
B: INTRON-ENCODED ENDONUCLEASE I-SCEI
C: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
D: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
E: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
H: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
I: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
J: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
K: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
L: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,38018
Polymers85,94010
Non-polymers4408
Water39622
1
A: INTRON-ENCODED ENDONUCLEASE I-SCEI
C: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
D: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
K: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
L: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2049
Polymers42,9845
Non-polymers2204
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8420 Å2
ΔGint-69.6 kcal/mol
Surface area15990 Å2
MethodPISA
2
B: INTRON-ENCODED ENDONUCLEASE I-SCEI
E: 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'
H: 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'
I: 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'
J: 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1769
Polymers42,9565
Non-polymers2204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-69.9 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.113, 80.565, 130.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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INTRON-ENCODED ENDONUCLEASE I- ... , 2 types, 2 molecules AB

#1: Protein INTRON-ENCODED ENDONUCLEASE I-SCEI / 21S RRNA INTRON MATURASE / HOMING ENDONUCLEASE OMEGA


Mass: 27717.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: SCEI, OMEGA, SECY, Q0160 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): PET24D / Variant (production host): ROSETTA PLYSS
References: UniProt: P03882, Hydrolases; Acting on ester bonds
#2: Protein INTRON-ENCODED ENDONUCLEASE I-SCEI / 21S RRNA INTRON MATURASE / HOMING ENDONUCLEASE OMEGA


Mass: 27689.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Gene: SCEI, OMEGA, SECY, Q0160 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): PET24D
References: UniProt: P03882, Hydrolases; Acting on ester bonds

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DNA chain , 4 types, 8 molecules CEDHILJK

#3: DNA chain 5'-D(*CP*AP*CP*GP*CP*TP*AP*GP*GP*GP*AP*TP*AP*AP)-3'


Mass: 4313.831 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*GP*GP*TP*AP*TP*TP*AP*CP*CP*CP*TP*GP*TP*TP *AP*TP)-3'


Mass: 4879.175 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(*CP*CP*CP*TP*AP*GP*CP*GP*TP)-3'


Mass: 2691.774 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#6: DNA chain 5'-D(*CP*AP*GP*GP*GP*TP*AP*AP*TP*AP*CP)-3'


Mass: 3382.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 30 molecules

#7: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.11 Å3/Da / Density % sol: 48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.89
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.9→43.62 Å / Num. obs: 36541 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Biso Wilson estimate: 61.56 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB NETRY 2VS8

2vs8


Resolution: 2.9→42.897 Å / SU ML: 0.39 / σ(F): 0.89 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 3649 10.19 %
Rwork0.1862 --
obs0.1926 36160 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→42.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 1982 8 22 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116046
X-RAY DIFFRACTIONf_angle_d1.2538587
X-RAY DIFFRACTIONf_dihedral_angle_d25.2522378
X-RAY DIFFRACTIONf_chiral_restr0.064940
X-RAY DIFFRACTIONf_plane_restr0.006747
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93820.4291500.33561259X-RAY DIFFRACTION100
2.9382-2.97840.37971390.32881266X-RAY DIFFRACTION100
2.9784-3.0210.35771370.29461220X-RAY DIFFRACTION100
3.021-3.06610.32861500.28241250X-RAY DIFFRACTION100
3.0661-3.11390.32341390.26231267X-RAY DIFFRACTION100
3.1139-3.1650.31381440.25481231X-RAY DIFFRACTION100
3.165-3.21950.30091380.23551283X-RAY DIFFRACTION100
3.2195-3.27810.28841370.231231X-RAY DIFFRACTION99
3.2781-3.34110.26261440.20711238X-RAY DIFFRACTION97
3.3411-3.40930.291290.20281212X-RAY DIFFRACTION98
3.4093-3.48340.28631340.19471266X-RAY DIFFRACTION99
3.4834-3.56440.26971370.20181220X-RAY DIFFRACTION100
3.5644-3.65340.24341500.19591296X-RAY DIFFRACTION100
3.6534-3.75220.2491450.19081225X-RAY DIFFRACTION100
3.7522-3.86250.28341390.19181234X-RAY DIFFRACTION100
3.8625-3.98710.26591440.18231247X-RAY DIFFRACTION100
3.9871-4.12950.26361340.18151260X-RAY DIFFRACTION100
4.1295-4.29470.21881370.15531262X-RAY DIFFRACTION100
4.2947-4.48990.23661480.1571261X-RAY DIFFRACTION100
4.4899-4.72640.21331290.15041276X-RAY DIFFRACTION100
4.7264-5.02210.21511410.16131235X-RAY DIFFRACTION100
5.0221-5.40920.23381490.15951259X-RAY DIFFRACTION100
5.4092-5.95220.18541440.151246X-RAY DIFFRACTION100
5.9522-6.81060.18771360.14871240X-RAY DIFFRACTION100
6.8106-8.56940.22831330.16421277X-RAY DIFFRACTION100
8.5694-42.90210.22431420.18741250X-RAY DIFFRACTION100

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