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- PDB-4yit: Crystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncl... -

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Basic information

Entry
Database: PDB / ID: 4yit
TitleCrystal Structure of LAGLIDADG Meganuclease I-AabMI Bound to Uncleaved DNA
Components
  • (DNA (25-MER)) x 3
  • DNA (25MER)
  • Meganuclease I-AabMI
Keywordshydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease
Function / homology
Function and homology information


endonuclease activity
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) / Meganuclease I-AabMI
Similarity search - Component
Biological speciesGremmeniella abietina (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.24 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 GM105691 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 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jun 15, 2016Group: Database references
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meganuclease I-AabMI
D: Meganuclease I-AabMI
B: DNA (25-MER)
C: DNA (25-MER)
E: DNA (25MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,34811
Polymers96,1486
Non-polymers2005
Water34219
1
A: Meganuclease I-AabMI
B: DNA (25-MER)
C: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5036
Polymers48,3833
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-78 kcal/mol
Surface area17460 Å2
MethodPISA
2
D: Meganuclease I-AabMI
E: DNA (25MER)
F: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8455
Polymers47,7653
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7990 Å2
ΔGint-73 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.960, 61.536, 88.621
Angle α, β, γ (deg.)97.180, 99.100, 101.890
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Meganuclease I-AabMI


Mass: 33027.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gremmeniella abietina (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A158RFF2*PLUS

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DNA chain , 4 types, 4 molecules BCEF

#2: DNA chain DNA (25-MER)


Mass: 7546.901 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (25-MER)


Mass: 7809.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (25MER)


Mass: 7257.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (25-MER)


Mass: 7479.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 24 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 550 MME, 20mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 1, 2014
RadiationMonochromator: Varimax HF Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.13→50 Å / Num. obs: 14205 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.101 / Χ2: 0.939 / Net I/av σ(I): 11.9 / Net I/σ(I): 7.8 / Num. measured all: 53531
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.13-3.243.40.32413550.8291.2
3.24-3.373.60.17513940.91494.7
3.37-3.533.70.16914070.93296
3.53-3.713.80.16514190.98297
3.71-3.943.80.15514131.03497.3
3.94-4.253.90.11614410.99497.5
4.25-4.673.90.08314471.00698.2
4.67-5.353.90.0814260.93598.3
5.35-6.743.90.08214660.96998.7
6.74-503.80.03314370.77598.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQY

3qqy


Resolution: 3.24→50 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.856 / SU B: 34.179 / SU ML: 0.575 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2988 651 5 %RANDOM
Rwork0.2253 ---
obs0.229 12412 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.56 Å2 / Biso mean: 48.001 Å2 / Biso min: 4.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å21.51 Å20.99 Å2
2---3.8 Å22.81 Å2
3---1.99 Å2
Refinement stepCycle: final / Resolution: 3.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4129 2009 5 19 6162
Biso mean--44.96 17.44 -
Num. residues----647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0166462
X-RAY DIFFRACTIONr_bond_other_d0.0020.024932
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6579162
X-RAY DIFFRACTIONr_angle_other_deg1.564311355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6555540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84423.708178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.66515650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8711520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026005
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021492
X-RAY DIFFRACTIONr_mcbond_it2.5885.0412187
X-RAY DIFFRACTIONr_mcbond_other2.5835.0422186
X-RAY DIFFRACTIONr_mcangle_it4.3157.5612718
LS refinement shellResolution: 3.24→3.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 56 -
Rwork0.259 825 -
all-881 -
obs--93.72 %

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