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- PDB-4z1z: Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable D... -

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Basic information

Entry
Database: PDB / ID: 4z1z
TitleCrystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTCT Central Four
Components
  • (DNA (28-MER)) x 2
  • Meganuclease I-SmaMI
Keywordshydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease
Function / homology
Function and homology information


endonuclease activity / mitochondrion / metal ion binding
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHallinan, J.P. / Stoddard, B.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM49857 United States
CitationJournal: Structure / Year: 2016
Title: Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Authors: Lambert, A.R. / Hallinan, J.P. / Shen, B.W. / Chik, J.K. / Bolduc, J.M. / Kulshina, N. / Robins, L.I. / Kaiser, B.K. / Jarjour, J. / Havens, K. / Scharenberg, A.M. / Stoddard, B.L.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meganuclease I-SmaMI
B: Meganuclease I-SmaMI
D: DNA (28-MER)
C: DNA (28-MER)
F: DNA (28-MER)
E: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,62514
Polymers102,9926
Non-polymers6338
Water724
1
A: Meganuclease I-SmaMI
D: DNA (28-MER)
C: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8127
Polymers51,4963
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-61 kcal/mol
Surface area18690 Å2
MethodPISA
2
B: Meganuclease I-SmaMI
F: DNA (28-MER)
E: DNA (28-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8127
Polymers51,4963
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-56 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.869, 179.282, 65.401
Angle α, β, γ (deg.)90.000, 95.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Meganuclease I-SmaMI


Mass: 34283.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus)
Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Production host: Escherichia coli (E. coli) / References: UniProt: F7WD42

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DNA chain , 2 types, 4 molecules DFCE

#2: DNA chain DNA (28-MER)


Mass: 8412.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (28-MER)


Mass: 8799.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 12 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 3550, 5mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.55 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 16992 / % possible obs: 98.5 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.061 / Rrim(I) all: 0.229 / Χ2: 1.164 / Net I/av σ(I): 13 / Net I/σ(I): 5.1 / Num. measured all: 234481
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.2110.90.71916660.8720.220.7550.72495.5
3.21-3.3411.80.50216260.9640.1470.5241.0496.7
3.34-3.4912.80.41817190.9790.120.4351.49698
3.49-3.6813.60.41316550.970.1150.4291.30398.2
3.68-3.9114.20.36117060.9640.0990.3751.26299
3.91-4.2114.70.2717280.9910.0720.2791.15299.4
4.21-4.63150.19517230.9950.0520.2021.14199.6
4.63-5.3150.16817070.9960.0450.1741.13399.7
5.3-6.67150.15717180.9960.0420.1631.11699.7
6.67-5014.80.098174410.0270.1011.17799.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOX

4lox


Resolution: 3.2→89.64 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.876 / SU B: 36.501 / SU ML: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.622 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 784 5 %RANDOM
Rwork0.2377 ---
obs0.2401 14881 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.17 Å2 / Biso mean: 44.818 Å2 / Biso min: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.32 Å20 Å2-4.79 Å2
2---2.44 Å20 Å2
3---6.56 Å2
Refinement stepCycle: final / Resolution: 3.2→89.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4335 2214 38 4 6591
Biso mean--64.62 28.74 -
Num. residues----697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0166952
X-RAY DIFFRACTIONr_bond_other_d0.0020.025279
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.669892
X-RAY DIFFRACTIONr_angle_other_deg1.318312166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34523.418158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.68615641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0721513
X-RAY DIFFRACTIONr_chiral_restr0.0850.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026403
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021592
X-RAY DIFFRACTIONr_mcbond_it2.9714.5332353
X-RAY DIFFRACTIONr_mcbond_other2.974.5322352
X-RAY DIFFRACTIONr_mcangle_it4.896.7952936
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 81 -
Rwork0.325 1041 -
all-1122 -
obs--96.23 %

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