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- PDB-4ncj: Crystal Structure of Pyrococcus furiosis Rad50 R805E mutation wit... -

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Basic information

Entry
Database: PDB / ID: 4ncj
TitleCrystal Structure of Pyrococcus furiosis Rad50 R805E mutation with ADP Beryllium Flouride
ComponentsDNA double-strand break repair Rad50 ATPase
KeywordsDNA BINDING PROTEIN / Adenosine Triphosphatase / DNA Repair / Fungal Protein
Function / homology
Function and homology information


double-strand break repair / ATP hydrolysis activity / zinc ion binding / ATP binding / identical protein binding
Similarity search - Function
AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...AAA domain, putative AbiEii toxin, Type IV TA system / DNA double-strand break repair Rad50 ATPase, archaeal type / Rad50 zinc hook motif / RAD50, zinc hook / Rad50 zinc-hook domain profile. / Rad50/SbcC-type AAA domain / AAA domain / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / DNA double-strand break repair Rad50 ATPase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsClassen, S. / Williams, G.J. / Arvai, A.S. / Williams, R.S.
CitationJournal: Embo J. / Year: 2014
Title: ATP-driven Rad50 conformations regulate DNA tethering, end resection, and ATM checkpoint signaling.
Authors: Deshpande, R.A. / Williams, G.J. / Limbo, O. / Williams, R.S. / Kuhnlein, J. / Lee, J.H. / Classen, S. / Guenther, G. / Russell, P. / Tainer, J.A. / Paull, T.T.
History
DepositionOct 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _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: DNA double-strand break repair Rad50 ATPase
B: DNA double-strand break repair Rad50 ATPase
C: DNA double-strand break repair Rad50 ATPase
D: DNA double-strand break repair Rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,39216
Polymers154,3224
Non-polymers2,07012
Water16,250902
1
A: DNA double-strand break repair Rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0984
Polymers38,5811
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA double-strand break repair Rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0984
Polymers38,5811
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA double-strand break repair Rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0984
Polymers38,5811
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA double-strand break repair Rad50 ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0984
Polymers38,5811
Non-polymers5183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.020, 108.482, 148.744
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
DNA double-strand break repair Rad50 ATPase


Mass: 38580.535 Da / Num. of mol.: 4 / Fragment: UNP residues 1-177 and 726-882 / Mutation: R805E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1167, rad50 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 (DE3) / References: UniProt: P58301
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: BeF3
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 902 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 100 mM Bicine, 6-14% PEG 20000, 2 mM Dioxane, pH 8.6, vapor diffusion, sitting drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97945
SYNCHROTRONALS 12.3.121.11583
Detector
TypeIDDetector
MARMOSAIC 325 mm CCD1CCD
MARMOSAIC 325 mm CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
2Si 111 DOUBLE CRYSTALSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
21.115831
ReflectionResolution: 2→50 Å / Num. obs: 172044 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.02 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.11
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.6542.02502641235394.8
2.05-2.110.5482.455355612742100
2.11-2.170.4552.99519101234899.9
2.17-2.230.6612.3418221069689.2
2.23-2.310.279.19353781012586.9
2.31-2.390.2525.54471601120099.9
2.39-2.480.1867.12459511084899.9
2.48-2.580.1558.64462310490100
2.58-2.690.12410.5942418997599.9
2.69-2.820.09713.4140515952999.9
2.82-2.980.07716.3338875913399.9
2.98-3.160.05522.136419857899.8
3.16-3.380.0428.6734174806199.8
3.38-3.650.03433.6330515748199.2
3.65-3.990.03137.2924022664195.8
3.99-4.470.02445.0425651620399.5
4.47-5.160.0248.1422394552899.5
5.16-6.320.02245.8420089465699.9
6.32-8.930.01947.7415343357599.9
8.930.01753.217920188295.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIXdev_1269refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→45.408 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8056 / SU ML: 0.29 / σ(F): 0.69 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 8701 5.09 %RANDOM
Rwork0.2233 ---
obs0.225 171047 97.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.3 Å2 / Biso mean: 43.3078 Å2 / Biso min: 12.05 Å2
Refinement stepCycle: LAST / Resolution: 2→45.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9887 0 128 902 10917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910342
X-RAY DIFFRACTIONf_angle_d1.24914003
X-RAY DIFFRACTIONf_chiral_restr0.0851621
X-RAY DIFFRACTIONf_plane_restr0.0051761
X-RAY DIFFRACTIONf_dihedral_angle_d15.2853865
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.01990.32962670.29884984525189
2.0199-2.04360.30172980.273855605858100
2.0436-2.06860.31883020.276755505852100
2.0686-2.09470.28262890.268655405829100
2.0947-2.12230.30053000.267956095909100
2.1223-2.15140.25662940.252355365830100
2.1514-2.18210.28662940.263455865880100
2.1821-2.21470.44392980.4375403570197
2.2147-2.24930.62421970.60343723392067
2.2493-2.28620.6211990.60494036423573
2.2862-2.32560.3572870.29865589587699
2.3256-2.36790.30472960.242655955891100
2.3679-2.41340.2943300.233655095839100
2.4134-2.46270.30882870.230855775864100
2.4627-2.51620.28233170.217755865903100
2.5162-2.57470.24023220.204155155837100
2.5747-2.63910.26732950.210255835878100
2.6391-2.71050.26462990.199155695868100
2.7105-2.79020.22422650.19356245889100
2.7902-2.88030.26843190.199455145833100
2.8803-2.98320.21463050.199955615866100
2.9832-3.10260.25562780.206955925870100
3.1026-3.24380.24613070.195155175824100
3.2438-3.41470.25252800.187956175897100
3.4147-3.62860.22842540.18455575582999
3.6286-3.90860.23563210.19455245556695
3.9086-4.30170.17483290.15825486581599
4.3017-4.92350.16022650.14555581584699
4.9235-6.20060.20173330.175855105843100
6.2006-45.42010.23852740.21685474574898
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)
13.00990.0679-0.91223.4825-0.54482.66570.1335-0.1387-0.10510.0427-0.17480.15390.1222-0.07070.03370.11390.0009-0.04130.1985-0.0310.183-13.185-40.803916.8344
21.6924-0.4588-0.3012.1830.17952.5031-0.0719-0.1841-0.00920.306-0.09080.52490.1485-0.4620.13030.2028-0.07010.01540.3653-0.10910.4032-22.8171-38.000922.3795
30.7418-0.34620.27273.1586-0.72753.85270.0338-0.20490.22660.44320.13710.0381-0.8776-0.1756-0.16150.33320.05980.0150.2747-0.06230.3012-17.6345-12.825613.7302
40.8319-0.01210.86171.3545-0.40453.45360.0082-0.04510.24660.1234-0.1226-0.4263-0.3340.40.12110.1738-0.0259-0.0670.3098-0.04770.3917-2.3653-28.427113.6078
53.83360.6342.36054.02920.32542.8019-0.1832-0.16810.0087-0.0812-0.05540.0705-0.00780.06750.24510.27910.00690.09940.219-0.00890.1907-5.6258-13.548592.1624
60.982-0.0830.61781.76430.51011.1039-0.1304-0.12330.00670.22850.0611-0.0929-0.0650.11790.07870.3527-0.05430.08550.32270.04670.24513.6087-16.326297.6797
71.32130.0143-0.10873.43271.16013.50.0856-0.1824-0.28260.5237-0.02330.08110.32570.1812-0.03870.3111-0.02930.04660.21270.04640.2245-2.7496-41.981788.3837
80.99920.687-0.07052.04070.22582.9254-0.0496-0.2019-0.12250.2934-0.2831.05520.2073-0.48880.15830.3098-0.08110.17470.3604-0.05970.4287-17.2065-25.366389.3911
92.59660.65240.96852.07190.60094.52150.10120.10950.342-0.20280.1222-0.2427-0.41270.0135-0.18340.17860.03610.05720.24330.06750.3251-14.6168-13.4711-14.3611
101.6393-0.24080.3062.1291-1.03443.80940.08510.48510.1432-0.25210.20220.1182-0.155-0.3431-0.26590.20520.03630.06370.45390.06820.3262-22.7528-16.7602-21.2897
110.2401-0.168-0.37971.3249-0.12861.4440.08090.1542-0.0737-0.5411-0.03690.18130.2925-0.0533-0.06390.38140.0415-0.13640.2578-0.0650.2663-16.582-42.3637-13.8309
120.551-0.5107-1.02112.9251-0.51833.82120.06580.05210.16340.042-0.1258-0.75970.23470.67550.03380.19010.05360.02180.4176-0.07010.4032-1.9585-23.6161-10.5702
132.4802-0.5797-1.39763.27820.92052.73020.01420.2308-0.3604-0.143-0.16120.33310.36890.06530.12110.2834-0.0053-0.0290.2229-0.06640.2206-7.7414-40.927160.3309
142.1137-0.9969-0.4792.13971.74293.4877-0.010.3891-0.1114-0.2853-0.19360.19940.03560.33030.18710.30810.051-0.03530.32720.01670.220.5336-37.761153.5342
150.5023-0.00410.19842.48720.66171.79420.05880.1260.0858-0.3478-0.1079-0.1177-0.51350.03160.01080.3271-0.0035-0.00150.19310.03020.2055-3.738-11.729661.3722
161.282-0.67740.4232.46860.44293.05540.010.1669-0.2146-0.0405-0.14370.77740.0137-0.50740.13490.1833-0.0002-0.04620.3082-0.06930.4102-19.2032-29.836365.2655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:60 )A1 - 60
2X-RAY DIFFRACTION2( CHAIN A AND RESID 61:163 )A61 - 163
3X-RAY DIFFRACTION3( CHAIN A AND RESID 735:822 )A735 - 822
4X-RAY DIFFRACTION4( CHAIN A AND RESID 823:882 )A823 - 882
5X-RAY DIFFRACTION5( CHAIN B AND RESID 1:60 )B1 - 60
6X-RAY DIFFRACTION6( CHAIN B AND RESID 61:164 )B61 - 164
7X-RAY DIFFRACTION7( CHAIN B AND RESID 736:822 )B736 - 822
8X-RAY DIFFRACTION8( CHAIN B AND RESID 823:882 )B823 - 882
9X-RAY DIFFRACTION9( CHAIN C AND RESID 1:60 )C1 - 60
10X-RAY DIFFRACTION10( CHAIN C AND RESID 61:163 )C61 - 163
11X-RAY DIFFRACTION11( CHAIN C AND RESID 726:822 )C726 - 822
12X-RAY DIFFRACTION12( CHAIN C AND RESID 823:882 )C823 - 882
13X-RAY DIFFRACTION13( CHAIN D AND RESID 1:60 )D1 - 60
14X-RAY DIFFRACTION14( CHAIN D AND RESID 61:164 )D61 - 164
15X-RAY DIFFRACTION15( CHAIN D AND RESID 726:822 )D726 - 822
16X-RAY DIFFRACTION16( CHAIN D AND RESID 823:882 )D823 - 882

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