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- PDB-4yhx: Crystal Structure of LAGLIDADG Meganuclease I-GpeMI Bound to Uncl... -

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Basic information

Entry
Database: PDB / ID: 4yhx
TitleCrystal Structure of LAGLIDADG Meganuclease I-GpeMI Bound to Uncleaved DNA
Components
  • (DNA (27-MER)) x 2
  • Ribosomal protein 3/homing endonuclease-like fusion protein
Keywordshydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease
Function / homology
Function and homology information


endonuclease activity / ribosome / 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) / Ribosomal protein 3/homing endonuclease-like fusion protein
Similarity search - Component
Biological speciesGrosmannia penicillata (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHallinan, J.P. / Kaiser, B.K. / 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
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 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 ...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 ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (27-MER)
C: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5706
Polymers51,4503
Non-polymers1203
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-91 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.985, 39.895, 73.986
Angle α, β, γ (deg.)90.000, 90.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribosomal protein 3/homing endonuclease-like fusion protein


Mass: 34857.055 Da / Num. of mol.: 1 / Fragment: unp residues 420-727
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grosmannia penicillata (fungus) / Gene: rps3/HEG fusion / Production host: Escherichia coli (E. coli) / References: UniProt: C7SQG1
#2: DNA chain DNA (27-MER)


Mass: 8049.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8543.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 22.5% PEG 3000, 50mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013
RadiationMonochromator: ASYMMETRIC CURVED CRYSTAL Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 24373 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Χ2: 1.181 / Net I/av σ(I): 11.281 / Net I/σ(I): 14.8 / Num. measured all: 84408
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.2330.45523660.7940.3010.5471.07697.6
2.23-2.323.40.43924370.8290.2780.5211.12299.6
2.32-2.423.50.3824060.8480.2380.4491.08199.9
2.42-2.553.60.29724450.9220.1850.3511.17699.9
2.55-2.713.60.22224210.9480.1370.2621.29199.8
2.71-2.923.60.16824220.9670.1040.1981.26699.7
2.92-3.213.60.11124470.9870.0690.1311.38899.8
3.21-3.683.60.07624560.9920.0480.091.30899.8
3.68-4.633.50.07724690.9910.0480.091.13699.7
4.63-503.30.05725040.9910.0360.0680.91897.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QQY

3qqy


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.573 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1237 5.1 %RANDOM
Rwork0.1779 ---
obs0.1812 23084 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 173.39 Å2 / Biso mean: 36.192 Å2 / Biso min: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å2-1.18 Å2
2--1.01 Å20 Å2
3---1.86 Å2
Refinement stepCycle: final / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2310 1101 3 219 3633
Biso mean--31.3 39.27 -
Num. residues----348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0163616
X-RAY DIFFRACTIONr_bond_other_d0.0010.022908
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.6595098
X-RAY DIFFRACTIONr_angle_other_deg1.04736724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6195296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68625.094106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11815433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.401159
X-RAY DIFFRACTIONr_chiral_restr0.090.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02818
X-RAY DIFFRACTIONr_mcbond_it2.6063.3211190
X-RAY DIFFRACTIONr_mcbond_other2.5913.3221185
X-RAY DIFFRACTIONr_mcangle_it3.7574.9731480
LS refinement shellResolution: 2.149→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 74 -
Rwork0.231 1567 -
all-1641 -
obs--89.77 %

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