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- PDB-4z20: Crystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable D... -

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Basic information

Entry
Database: PDB / ID: 4z20
TitleCrystal Structure of Meganuclease I-SmaMI Bound to Uncleaveable DNA with a TTGT Central Four
Components
  • (DNA (26-MER)) x 2
  • MEGANUCLEASE I-SMAMI
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) / Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHallinan, J.P. / Stoddard, B.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) 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 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 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_conn.ptnr2_label_seq_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
A: MEGANUCLEASE I-SMAMI
C: DNA (26-MER)
B: DNA (26-MER)
D: MEGANUCLEASE I-SMAMI
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,87711
Polymers100,5206
Non-polymers3565
Water19811
1
A: MEGANUCLEASE I-SMAMI
C: DNA (26-MER)
B: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3925
Polymers50,2603
Non-polymers1322
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MEGANUCLEASE I-SMAMI
F: DNA (26-MER)
E: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4846
Polymers50,2603
Non-polymers2243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.690, 172.262, 59.994
Angle α, β, γ (deg.)90.000, 92.360, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12C
22F
13B
23E

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUGLYGLYAA8 - 3009 - 301
21LEULEUGLYGLYDD8 - 3009 - 301
12DCDCDCDCCB1 - 261 - 26
22DCDCDCDCFE1 - 261 - 26
13DGDGDGDGBC1 - 261 - 26
23DGDGDGDGEF1 - 261 - 26

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.173049, -0.000417, -0.984913), (-0.016108, -0.999865, 0.003253), (-0.984781, 0.016428, 0.173019)77.233177, 33.690708, 76.140663
3given(1), (1), (1)
4given(-0.183606, 7.8E-5, -0.983), (-0.009019, -0.999958, 0.001605), (-0.982958, 0.009161, 0.183599)77.169601, 33.869049, 75.989754
5given(1), (1), (1)
6given(-0.187852, -0.000228, -0.982197), (-0.012371, -0.99992, 0.002598), (-0.982119, 0.012639, 0.187834)77.078827, 33.792938, 75.68586

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein MEGANUCLEASE I-SMAMI


Mass: 34283.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus)
Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Production host: Escherichia coli (E. coli) / References: UniProt: F7WD42

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DNA chain , 2 types, 4 molecules CFBE

#2: DNA chain DNA (26-MER)


Mass: 7850.054 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (26-MER)


Mass: 8126.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 16 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.35 Å3/Da / Density % sol: 47.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 25% PEG 2000 MME, 5mM 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 RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→86.13 Å / Num. obs: 18370 / % possible obs: 98.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.039 / Rrim(I) all: 0.075 / Χ2: 1.297 / Net I/av σ(I): 16.928 / Net I/σ(I): 19.3 / Num. measured all: 69222
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.113.70.79518010.8050.4780.9291.51198.3
3.11-3.233.80.48718480.9430.290.5671.48798.6
3.23-3.383.80.22918070.9920.1390.2681.54598.7
3.38-3.563.80.1918380.9910.1150.2221.46399.1
3.56-3.783.80.16218290.9940.0960.1881.43499
3.78-4.073.80.10118400.9950.060.1181.21499.1
4.07-4.483.80.06618300.9970.0390.0771.09499
4.48-5.133.80.04318670.9980.0260.0511.03999.7
5.13-6.463.80.03818410.9980.0230.0451.18299.2
6.46-503.70.02518690.9990.0150.0291.00998.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOX

4lox


Resolution: 3.2→86.13 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 87.311 / SU ML: 0.645 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.638 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2912 753 5 %RANDOM
Rwork0.2333 ---
obs0.2361 14420 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 439.61 Å2 / Biso mean: 188.585 Å2 / Biso min: 99.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.15 Å20 Å2-2.08 Å2
2--1.2 Å20 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 3.2→86.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 2132 20 11 6503
Biso mean--428.3 429.34 -
Num. residues----693
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0166849
X-RAY DIFFRACTIONr_bond_other_d0.0060.025220
X-RAY DIFFRACTIONr_angle_refined_deg1.3431.6629737
X-RAY DIFFRACTIONr_angle_other_deg1.918312026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3055585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.4623.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.1915644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5981513
X-RAY DIFFRACTIONr_chiral_restr0.0820.21002
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026364
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021581
X-RAY DIFFRACTIONr_mcbond_it4.4499.7042351
X-RAY DIFFRACTIONr_mcbond_other4.4459.7032350
X-RAY DIFFRACTIONr_mcangle_it7.32914.5572932
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A22507.45
2C4806.36
3B46813.87
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 56 -
Rwork0.321 1046 -
all-1102 -
obs--99.01 %
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)
10.77910.12670.29074.16940.30010.1445-0.04340.43570.03030.0530.15440.3862-0.03830.159-0.1111.3440.01730.08670.9392-0.05111.05513.1162.720689.3181
20.61820.02150.36270.0618-0.04030.43280.29160.24640.14480.2792-0.10520.02020.12120.4749-0.18641.548-0.01290.08050.6758-0.05971.219823.51855.247890.4198
30.80430.62380.73190.93780.50090.82160.4230.4060.03261.14720.0153-0.14250.14840.4008-0.43831.9948-0.01790.20820.30660.03421.261623.49952.186891.3818
40.37630.47630.36893.1509-0.33220.6799-0.0975-0.019-0.0488-0.00350.06320.0722-0.03330.16190.03431.3213-0.01830.1580.82550.12281.1688-0.979431.427464.872
50.021-0.12720.0222.4961-0.32571.15850.0308-0.03660.1033-0.2792-0.1880.09610.1695-0.12530.15711.37960.001-0.00120.50730.06891.4256-4.069128.74755.3449
60.1166-0.02660.3770.044-0.11141.4737-0.02740.0435-0.0253-0.1742-0.0370.15630.09570.43540.06441.63790.06450.07220.36420.19281.5771-4.952631.808955.4926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 302
2X-RAY DIFFRACTION2C1 - 26
3X-RAY DIFFRACTION3B1 - 26
4X-RAY DIFFRACTION4D8 - 301
5X-RAY DIFFRACTION5F1 - 26
6X-RAY DIFFRACTION6E1 - 26

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