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- PDB-4z1x: Crystal structure of LAGLIDADG homing endonuclease I-GzeII in com... -

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Basic information

Entry
Database: PDB / ID: 4z1x
TitleCrystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target
Components
  • (DNA (27-MER)) x 2
  • LAGLIDADG endonuclease
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) / LAGLIDADG endonuclease
Similarity search - Component
Biological speciesFusarium graminearum PH-1 (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsStoddard, B.L. / Lambert, A.R. / Kulshina, N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM49857 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)RL1 CA133833 United States
CitationJournal: To Be Published
Title: Crystal structure of LAGLIDADG homing endonuclease I-GzeII in complex with DNA target
Authors: Stoddard, B.L. / Lambert, A.R. / Kulshina, N.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_entity_src_syn / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (27-MER)
D: DNA (27-MER)
E: DNA (27-MER)
F: DNA (27-MER)
A: LAGLIDADG endonuclease
B: LAGLIDADG endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,63910
Polymers102,4796
Non-polymers1604
Water2,324129
1
C: DNA (27-MER)
D: DNA (27-MER)
B: LAGLIDADG endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3195
Polymers51,2393
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8050 Å2
ΔGint-80 kcal/mol
Surface area19100 Å2
MethodPISA
2
E: DNA (27-MER)
F: DNA (27-MER)
A: LAGLIDADG endonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3195
Polymers51,2393
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-75 kcal/mol
Surface area19480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.833, 61.186, 128.871
Angle α, β, γ (deg.)90.000, 116.300, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-527-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21E
12D
22F
13A
23B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DGDGDGDGCA1 - 271 - 27
21DGDGDGDGEC1 - 271 - 27
12DCDCDCDCDB1 - 261 - 26
22DCDCDCDCFD1 - 261 - 26
13SERSERLYSLYSAE6 - 2965 - 295
23SERSERLYSLYSBF6 - 2965 - 295

NCS ensembles :
ID
1
2
3

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Components

#1: DNA chain DNA (27-MER)


Mass: 8445.457 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (27-MER)


Mass: 8147.261 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein LAGLIDADG endonuclease / I-GzeII


Mass: 34646.625 Da / Num. of mol.: 2 / Mutation: L96K, I104N, L154K, V202S, I203N, V211N, L313K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium graminearum PH-1 (fungus) / Gene: nad2 / Production host: Escherichia coli (E. coli) / References: UniProt: A5J036
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.22 Å3/Da / Density % sol: 44.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 6000 0.1M HEPES pH 7.5 2mM CaCl2 26bp duplex DNA with single base 3' overhang

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→115.526 Å / Num. obs: 20664 / % possible obs: 98.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 22.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.8 / % possible all: 90

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3qqy


Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.2273 / WRfactor Rwork: 0.1667 / FOM work R set: 0.8254 / SU B: 29.61 / SU ML: 0.278 / SU R Cruickshank DPI: 0.2854 / SU Rfree: 0.3965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1113 5.1 %RANDOM
Rwork0.173 ---
obs0.1764 20664 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 196.96 Å2 / Biso mean: 41.118 Å2 / Biso min: 10.72 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-2.21 Å2
2--2.15 Å20 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4603 2170 4 129 6906
Biso mean--28.17 30.01 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0167161
X-RAY DIFFRACTIONr_bond_other_d0.0040.025645
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.65410104
X-RAY DIFFRACTIONr_angle_other_deg1.298313048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30524.155207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.115826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8621518
X-RAY DIFFRACTIONr_chiral_restr0.0870.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021664
X-RAY DIFFRACTIONr_mcbond_it1.6572.4442335
X-RAY DIFFRACTIONr_mcbond_other1.6522.4432332
X-RAY DIFFRACTIONr_mcangle_it2.8773.6652904
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C41590.07
12E41590.07
21D39320.04
22F39320.04
31A338940.07
32B338940.07
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 87 -
Rwork0.269 1283 -
all-1370 -
obs--87.09 %
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)
10.21880.10410.47340.3142-0.29183.9561-0.1011-0.0302-0.1002-0.0505-0.04-0.0729-0.16450.25910.14110.13480.00380.05340.13560.07690.1009-18.780832.8331-16.4708
20.16450.08330.22330.3362-0.05234.1677-0.0577-0.0446-0.1321-0.02990.0355-0.0004-0.23870.3920.02220.1669-0.01360.01730.10630.0820.1387-18.317233.7188-15.9579
30.56760.02390.76270.8745-1.10153.3070.1438-0.07250.00620.04290.21960.1043-0.1114-0.2086-0.36330.1366-0.03320.08910.1576-0.01090.0869-15.99420.3571-41.0123
40.3048-0.0451.11730.4406-0.59395.20310.0128-0.055-0.02440.0870.15860.1141-0.2951-0.2756-0.17140.11360.0063-0.0010.08020.04830.1608-16.63551.3627-41.6817
50.32810.18890.46320.59590.44491.94140.02580.0296-0.00820.00510.0349-0.0688-0.02340.0075-0.06080.0495-0.00930.00150.0482-0.01960.2064-7.7141-2.444-45.5535
60.5633-0.23520.37810.385-0.95732.8175-0.0707-0.0053-0.0307-0.01890.01450.06690.12760.06270.05620.14130.01460.00430.02610.06340.1647-26.49827.5882-12.5649
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 27
2X-RAY DIFFRACTION2D1 - 103
3X-RAY DIFFRACTION3E1 - 103
4X-RAY DIFFRACTION4F1 - 106
5X-RAY DIFFRACTION5A6 - 507
6X-RAY DIFFRACTION6B6 - 501

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