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- PDB-5eaw: Crystal structure of Dna2 nuclease-helicase -

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Basic information

Entry
Database: PDB / ID: 5eaw
TitleCrystal structure of Dna2 nuclease-helicase
ComponentsDNA replication ATP-dependent helicase/nuclease DNA2
KeywordsHYDROLASE / DNA binding protein
Function / homology
Function and homology information


Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA replication, Okazaki fragment processing / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / gamma DNA polymerase complex ...Removal of the Flap Intermediate / Removal of the Flap Intermediate from the C-strand / Homologous DNA Pairing and Strand Exchange / Presynaptic phase of homologous DNA pairing and strand exchange / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA replication, Okazaki fragment processing / HDR through Single Strand Annealing (SSA) / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / gamma DNA polymerase complex / Processing of DNA double-strand break ends / site-specific endodeoxyribonuclease activity, specific for altered base / mitochondrial DNA replication / mitotic telomere maintenance via semi-conservative replication / nucleic acid metabolic process / 5'-flap endonuclease activity / DNA replication, removal of RNA primer / DNA double-strand break processing / nuclease activity / Regulation of TP53 Activity through Phosphorylation / DNA replication checkpoint signaling / replication fork reversal / single-stranded DNA helicase activity / mitochondrial DNA repair / mitochondrial nucleoid / telomere maintenance / positive regulation of DNA replication / base-excision repair / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / DNA helicase / DNA replication / chromosome, telomeric region / Hydrolases; Acting on ester bonds / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / PD-(D/E)XK endonuclease-like domain superfamily ...: / Dna2 Rift barrel domain / DNA replication factor Dna2, N-terminal / DNA replication ATP-dependent helicase/nuclease Dna2 / DNA replication factor Dna2 / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / PD-(D/E)XK endonuclease-like domain superfamily / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / IRON/SULFUR CLUSTER / DNA replication ATP-dependent helicase/nuclease DNA2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsZhou, C. / Pourmal, S. / Pavletich, N.P.
CitationJournal: Elife / Year: 2015
Title: Dna2 nuclease-helicase structure, mechanism and regulation by Rpa.
Authors: Zhou, C. / Pourmal, S. / Pavletich, N.P.
History
DepositionOct 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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_struct_oper_list / 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_oper_list.symmetry_operation / _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
Revision 1.2Mar 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: DNA replication ATP-dependent helicase/nuclease DNA2
B: DNA replication ATP-dependent helicase/nuclease DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,4156
Polymers237,8572
Non-polymers1,5584
Water0
1
A: DNA replication ATP-dependent helicase/nuclease DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7073
Polymers118,9291
Non-polymers7792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA replication ATP-dependent helicase/nuclease DNA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,7073
Polymers118,9291
Non-polymers7792
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.900, 148.600, 170.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22A
13B
23A
14B
24A
15B
25A
16B
26A
17A
27B
18A
28B

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
11METMETGLUGLUBB1 - 131 - 13
21METMETGLUGLUAA1 - 131 - 13
12VALVALTYRTYRBB21 - 12121 - 121
22VALVALTYRTYRAA21 - 12121 - 121
13PROPROLYSLYSBB122 - 460122 - 460
23PROPROLYSLYSAA122 - 460122 - 460
14THRTHRLEULEUBB461 - 563461 - 563
24THRTHRLEULEUAA461 - 563461 - 563
15HISHISVALVALBB569 - 826569 - 826
25HISHISVALVALAA569 - 826569 - 826
16GLNGLNLEULEUBB827 - 1056827 - 1056
26GLNGLNLEULEUAA827 - 1056827 - 1056
17ARGARGARGARGAA600600
27ARGARGARGARGBB600600
18GLNGLNGLNGLNAA502502
28GLNGLNGLNGLNBB502502

NCS ensembles :
ID
1
2
3
4
5
6
7
8

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999958, -0.00918, 0.000728), (0.009124, -0.998353, -0.056644), (0.001247, -0.056635, 0.998394)178.981415, 5.92617, 2.06971
3given(1), (1), (1)
4given(-0.999971, 0.007622, -0.000803), (-0.007624, -0.999968, 0.002544), (-0.000783, 0.00255, 0.999996)179.375519, 0.18174, -0.85494
5given(1), (1), (1)
6given(-0.999941, 0.004195, 0.01001), (-0.004179, -0.99999, 0.001597), (0.010017, 0.001556, 0.999949)178.463303, 0.10816, -1.39736
7given(1), (1), (1)
8given(-0.99994, 0.010012, 0.004376), (-0.010028, -0.999943, -0.003651), (0.004339, -0.003695, 0.999984)178.929947, 0.78992, -1.14148
9given(1), (1), (1)
10given(-0.999236, -0.003224, 0.038943), (0.003347, -0.99999, 0.003088), (0.038933, 0.003216, 0.999237)176.208405, -0.54603, -3.4447
11given(1), (1), (1)
12given(-0.998659, -0.004474, 0.051572), (0.005392, -0.999829, 0.017671), (0.051484, 0.017926, 0.998513)175.408371, -1.63426, -4.93277
13given(1), (1), (1)
14given(-0.99243, -0.086216, 0.087462), (0.085383, -0.99626, -0.013228), (0.088275, -0.00566, 0.99608)169.458878, -8.09995, -8.82755
15given(1), (1), (1)
16given(-0.998588, 0.005368, 0.052845), (0.001459, -0.991732, 0.128316), (0.053097, 0.128212, 0.990324)175.327011, -6.67202, -0.60696

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Components

#1: Protein DNA replication ATP-dependent helicase/nuclease DNA2 / DNA replication ATP-dependent helicase-like homolog


Mass: 118928.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dna2, Dna2l, Kiaa0083 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q6ZQJ5, Hydrolases; Acting on ester bonds, DNA helicase
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 80 mm MES pH 6.5, 250 mM Li2SO4, 8-12% PEG MME 5000, 2 mM MgCl2
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 61754 / % possible obs: 98.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.068 / Rrim(I) all: 0.149 / Χ2: 0.64 / Net I/av σ(I): 7.933 / Net I/σ(I): 4.1 / Num. measured all: 274504
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3-3.114.50.78761330.7080.4190.8970.65298.9
3.11-3.234.40.56261360.8130.30.6410.65999
3.23-3.384.30.3961370.9080.2080.4450.66598.6
3.38-3.564.20.26960150.9470.1450.3080.65697.1
3.56-3.784.60.20161950.9750.1040.2270.65499.4
3.78-4.074.60.13561820.9890.0690.1530.64999.1
4.07-4.484.40.09361400.9940.0480.1060.61797.9
4.48-5.134.50.07161860.9970.0360.080.61998
5.13-6.464.50.07962480.9960.040.0890.62698.2
6.46-504.30.03863820.9990.020.0430.60396.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHARPphasing
RefinementResolution: 3→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.482 / SU ML: 0.355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2468 1388 2.5 %RANDOM
Rwork0.2092 ---
obs0.2102 54064 89.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 205.78 Å2 / Biso mean: 63.636 Å2 / Biso min: 20.28 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0 Å2
2---3.11 Å20 Å2
3---4.19 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16542 0 70 0 16612
Biso mean--86.44 --
Num. residues----2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01916924
X-RAY DIFFRACTIONr_angle_refined_deg1.71.98922912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5552084
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77123.612742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.946153112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.34915144
X-RAY DIFFRACTIONr_chiral_restr0.1190.22632
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112492
X-RAY DIFFRACTIONr_mcbond_it3.9826.2498360
X-RAY DIFFRACTIONr_mcangle_it6.6059.3610436
X-RAY DIFFRACTIONr_scbond_it4.4856.4158564
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 99

Ens-IDNumberRms dev position (Å)
11066.85
28128.25
326894.21
47987.53
520212.37
617924.05
783.57
8274.34
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 91 -
Rwork0.359 3389 -
all-3480 -
obs--76.94 %

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