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- PDB-5esp: Crystal Structure of LAGLIDADG Meganuclease I-PanMI with coordina... -

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Basic information

Entry
Database: PDB / ID: 5esp
TitleCrystal Structure of LAGLIDADG Meganuclease I-PanMI with coordinated Calcium ions
Components
  • (DNA (27-MER)) x 2
  • I-PanMI
KeywordsHYDROLASE/DNA / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease
Function / homology
Function and homology information


endonuclease activity / mitochondrion
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) / Uncharacterized 49.1 kDa protein in ND3 intron
Similarity search - Component
Biological speciesPodospora anserina (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.995 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)NIH 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
DepositionNov 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Data collection / Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Sep 13, 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 1.4Dec 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
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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: I-PanMI
B: I-PanMI
G: DNA (27-MER)
H: DNA (27-MER)
C: DNA (27-MER)
D: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,52312
Polymers101,1796
Non-polymers3456
Water362
1
A: I-PanMI
G: DNA (27-MER)
H: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7626
Polymers50,5893
Non-polymers1723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-88 kcal/mol
Surface area18550 Å2
MethodPISA
2
B: I-PanMI
C: DNA (27-MER)
D: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7626
Polymers50,5893
Non-polymers1723
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-90 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.555, 78.442, 101.023
Angle α, β, γ (deg.)90.000, 92.380, 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 I-PanMI


Mass: 33995.645 Da / Num. of mol.: 2 / Fragment: UNP residues 136-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Podospora anserina (fungus) / Strain: S / ATCC MYA-4624 / DSM 980 / FGSC 10383 / Production host: Escherichia coli (E. coli) / References: UniProt: P15563

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DNA chain , 2 types, 4 molecules GCHD

#2: DNA chain DNA (27-MER)


Mass: 8092.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8501.480 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 8 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 28% PEG 3350, 5mM Calcium Chloride

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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: Sep 10, 2015
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: 2.995→30.969 Å / Num. obs: 21733 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.07 / Rrim(I) all: 0.173 / Χ2: 1.518 / Net I/av σ(I): 13.226 / Net I/σ(I): 7.7 / Num. measured all: 127010
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.115.80.8521130.7070.3810.9331.44197.7
3.11-3.235.80.58321300.8250.2610.641.40998
3.23-3.385.90.35721730.9410.160.3911.44698.1
3.38-3.565.90.3421550.9080.150.3721.78798.6
3.56-3.785.90.25121630.8610.1110.2751.60698.5
3.78-4.075.90.23321650.9560.1040.2561.75598.8
4.07-4.485.90.11621690.9910.0520.1271.48399
4.48-5.135.90.08722080.9960.0390.0961.42999.2
5.13-6.465.80.08922050.9950.040.0981.47899.6
6.46-505.70.04922520.9980.0230.0541.34498.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JEE

4jee
PDB Unreleased entry


Resolution: 2.995→30.969 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 1989 9.13 %
Rwork0.2256 --
obs0.2296 21733 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 227.68 Å2 / Biso mean: 56.0929 Å2 / Biso min: 10.41 Å2
Refinement stepCycle: final / Resolution: 2.995→30.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 2195 32 2 6739
Biso mean--42.73 36.99 -
Num. residues----687

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