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- PDB-3fd2: Crystal structure of mMsoI/DNA complex with calcium -

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Basic information

Entry
Database: PDB / ID: 3fd2
TitleCrystal structure of mMsoI/DNA complex with calcium
Components
  • 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
  • Site-specific DNA endonuclease I-MsoI
KeywordsHYDROLASE/DNA / Protein-DNA complex / Chloroplast / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


chloroplast / endonuclease activity / 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) / Site-specific DNA endonuclease I-MsoI
Similarity search - Component
Biological speciesMonomastix sp. (plant)
Monomastix sp. OKE-1
unidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsLi, H. / Monnat, R.J.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.
Authors: Li, H. / Pellenz, S. / Ulge, U. / Stoddard, B.L. / Monnat, R.J.
History
DepositionNov 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jun 28, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _struct_ref_seq.db_align_beg ..._entity.pdbx_description / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg
Revision 1.4Sep 6, 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 / struct_site
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 / _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: Site-specific DNA endonuclease I-MsoI
B: 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
C: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8475
Polymers56,7673
Non-polymers802
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-74 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.932, 41.933, 70.960
Angle α, β, γ (deg.)107.21, 95.43, 109.44
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Site-specific DNA endonuclease I-MsoI


Mass: 42024.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: fusion protein comprises residues 1-170 of I-MSOI, a linker of 33 residues (TGSGSGSKHPTLTLPTTTSQENLPNGSGSGSGT) and a 2nd I-MSOI (1-170 residues).
Source: (gene. exp.) Monomastix sp. (strain OKE-1) (plant), (gene. exp.) Monomastix sp. OKE-1, unidentified
Strain: OKE-1
Gene: orf170, the chloroplast large subunit rDNA intron gene
Plasmid: pET system / Production host: Escherichia coli (E. coli) / Strain (production host): C2566
References: UniProt: C0JWR6, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'


Mass: 7419.792 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the physiological DNA target site of I-MsoI in the chloroplast large subunit rDNA of Monomastix
Source: (synth.) synthetic construct (others)
#3: DNA chain 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'


Mass: 7321.716 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the physiological DNA target site of I-MsoI in the chloroplast large subunit rDNA of Monomastix
Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence details33 RESIDUES OF LINKER (TGSGSGSKHPTLTLPTTTSQENLPNGSGSGSGT) INSERTED BETWEEN TWO I-MSOI PROTEINS

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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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 291 K / pH: 7.3
Details: 22% PEG 400, 100 mM Tris pH 7.3, 10 mM calcium chloride, 20 mM sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 11073 / % possible obs: 97 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 21
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 4.51 / % possible all: 95.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M5X

1m5x


Resolution: 2.69→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.901 / SU ML: 0.422 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 546 4.8 %RANDOM
Rwork0.211 ---
obs0.215 10862 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å24.6 Å2-6.76 Å2
2--1.75 Å2-3.57 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.69→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 978 2 35 3735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.064
X-RAY DIFFRACTIONr_gen_planes_refined0.003
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.304
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.142
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 37 -
Rwork0.294 749 -
obs--90.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8289-0.04763.13881.616-1.604516.9580.2676-0.0824-0.27250.01340.2930.1840.1332-0.2923-0.5606-0.23-0.02790.0697-0.2531-0.01560.080316.300713.7601-7.5468
24.0403-1.18614.82171.8423-1.733718.44471.1348-0.6091-0.8251-0.37180.58430.53922.7998-2.0788-1.71910.0243-0.5052-0.2767-0.26440.25190.145711.48526.2318-8.4028
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 178
2X-RAY DIFFRACTION1A207 - 367
3X-RAY DIFFRACTION2B501 - 524
4X-RAY DIFFRACTION2C551 - 574

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